Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
You can convert Dicom using MRICroN with the dcm2nii utility
shantanu
On Mon, April 28, 2014 6:55 pm, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though had to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says that the unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for volume view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get the following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri convert and recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition acquired at the time of experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though had to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says that the unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for volume view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get the following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri convert and recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition acquired at the time of experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though
had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says that the unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for volume view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get the following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri convert
and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error.
My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be very grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though
had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri convert
and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the
Applications/freesurfer
directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui
and
it is not able to convert the mri dcm files. Then I shifted to
UNIX
and again it is saying error.
My file is on the desktop and I have given it subject id as Grace.
My
directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file
conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be
very
grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom
it is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software,
though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
open
file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri
convert and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of
experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you
want
the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the
Applications/freesurfer
directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files
to
convert. However, before I was using Jamaan Alghamadi created gui
and
it is not able to convert the mri dcm files. Then I shifted to
UNIX
and again it is saying error.
My file is on the desktop and I have given it subject id as Grace.
My
directory to the dcm file is '/Users/sampada/desktop/Grace.
My terminal look like this before I proceed with the file
conversion
Last login: Mon Apr 28 15:10:13 on ttys001
dhcp020-223-179:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Will anyone please let me know what I am doing wrong? I will be
very
grateful for any input.
Thanks and regards,
Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom
it is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software,
though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
open
file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri
convert and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of
experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you
want
the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > Hello I have only recently started the fmri data analysis and I > downloaded freesurfer point by point from martinos site and > incorporated the license file as well into the
Applications/freesurfer
> directory. I have run into the first problem and that is of data > conversion. My file is in dcm format and I have 11,000 dcm files
to
> convert. However, before I was using Jamaan Alghamadi created gui
and
> it is not able to convert the mri dcm files. Then I shifted to
UNIX
> and again it is saying error. > > My file is on the desktop and I have given it subject id as Grace.
My
> directory to the dcm file is '/Users/sampada/desktop/Grace. > > My terminal look like this before I proceed with the file
conversion
> > Last login: Mon Apr 28 15:10:13 on ttys001 > > dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > > dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > > > Will anyone please let me know what I am doing wrong? I will be
very
> grateful for any input. > > > Thanks and regards, > > > Sampada > Senior research support specialist > Molecular and neuroimaging department > Department of Psychiatry > 451, biomedical research building > University at Buffalo (south campus) > Buffalo, NY-14216 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom
it is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sampada
the recon-all script is designed to analyze T1-weighted structural data. Once that has been done, it can be used to facilitate fMRI analysis. Is that what you are trying to do? What are the 8 volumes?
cheers Bruce
On Fri, 9 May 2014, Dr Sampada Sinha wrote:
Hello Freesurfer, Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh shantanu@nmr.mgh.harvard.edu wrote: sorry
try: cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.niisampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software,
though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
open
file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri
convert and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of
experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you
want
the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > Hello I have only recently started the fmri data analysis and I > downloaded freesurfer point by point from martinos site and > incorporated the license file as well into the
Applications/freesurfer
> directory. I have run into the first problem and that is of data > conversion. My file is in dcm format and I have 11,000 dcm files
to
> convert. However, before I was using Jamaan Alghamadi created gui
and
> it is not able to convert the mri dcm files. Then I shifted to
UNIX
> and again it is saying error. > > My file is on the desktop and I have given it subject id as Grace.
My
> directory to the dcm file is '/Users/sampada/desktop/Grace. > > My terminal look like this before I proceed with the file
conversion
> > Last login: Mon Apr 28 15:10:13 on ttys001 > > dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > > dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > > > Will anyone please let me know what I am doing wrong? I will be
very
> grateful for any input. > > > Thanks and regards, > > > Sampada > Senior research support specialist > Molecular and neuroimaging department > Department of Psychiatry > 451, biomedical research building > University at Buffalo (south campus) > Buffalo, NY-14216 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom
it is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give
to
free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software,
though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I
get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
open
file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri
convert and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of
experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu > wrote:
> > Have you tried using dcmunpack? You run it twice, once without
any
> output to get a list of runs in the folder. The 2nd with how you
want
> the data converted. Run it with --help to get more info > doug > > On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > > Hello I have only recently started the fmri data analysis and I > > downloaded freesurfer point by point from martinos site and > > incorporated the license file as well into the
Applications/freesurfer
> > directory. I have run into the first problem and that is of
data
> > conversion. My file is in dcm format and I have 11,000 dcm
files
to
> > convert. However, before I was using Jamaan Alghamadi created
gui
and
> > it is not able to convert the mri dcm files. Then I shifted to
UNIX
> > and again it is saying error. > > > > My file is on the desktop and I have given it subject id as
Grace.
My
> > directory to the dcm file is '/Users/sampada/desktop/Grace. > > > > My terminal look like this before I proceed with the file
conversion
> > > > Last login: Mon Apr 28 15:10:13 on ttys001 > > > > dhcp020-223-179:~ sampada$ export > FREESURFER_HOME=/Applications/freesurfer > > > > dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /Applications/freesurfer > > > > FSFAST_HOME /Applications/freesurfer/fsfast > > > > FSF_OUTPUT_FORMAT nii.gz > > > > SUBJECTS_DIR /Applications/freesurfer/subjects > > > > MNI_DIR /Applications/freesurfer/mni > > > > > > > > Will anyone please let me know what I am doing wrong? I will be
very
> > grateful for any input. > > > > > > Thanks and regards, > > > > > > Sampada > > Senior research support specialist > > Molecular and neuroimaging department > > Department of Psychiatry > > 451, biomedical research building > > University at Buffalo (south campus) > > Buffalo, NY-14216 > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to
whom
> it > is > addressed. If you believe this e-mail was sent to you in error
and
the
> e-mail > contains patient information, please contact the Partners
Compliance
> HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent
to
you
> in > error > but does not contain patient information, please contact the
sender
and
> properly > dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello freesurfer, thanks for your message. I am doing the recon-all for T1 and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am running this command for recon-all '-all' process. My two files (T1 and T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give
to
free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > *Hello freesurfer* > > *Sorry for the personal message Shantanu. * > > *I managed to convert my dicom to nifti using mricron software, though had > to make some changes to the preferences. * > > *About the dcmunpack: The user manual on dcmunpack on fs site says that > the > unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips > infinity for our PET scan.* > > *I am very new to Unix, free surfer and neuroimaging, so couldn't > understand what nipy would do...* > > *My FS is working fine as when I typed tkmedit bert orig.mngz for volume > view it was displaying image.* > > *But the when I tried to convert my .nii files to .mgz format , I
get
the > following error:* > > > Last login: Tue May 6 10:40:32 on ttys000 > dhcp020-222-117:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > dhcp020-222-117:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > dhcp020-222-117:~ sampada$ mri_convert > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > '/Users/sampada/Desktop/test/mri/org/.mgz' > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii > /Users/sampada/Desktop/test/mri/org/.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0.0268034, -0.99958, 0.0110098) > j_ras = (0.0381548, 0.0120287, 0.999199) > k_ras = (0.998912, 0.0263618, -0.0384612) > writing to /Users/sampada/Desktop/test/mri/org/.mgz... > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open > file > > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz > > > *Will you please let me know what command I need to use to mri convert and > recon all of my files? * > I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 > (in the order of the acquisition acquired at the time of experiment).* > > > *Thanks and regards,* > > *Sampada* > > > > > > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu >> wrote: > >> >> Have you tried using dcmunpack? You run it twice, once without
any
>> output to get a list of runs in the folder. The 2nd with how you want >> the data converted. Run it with --help to get more info >> doug >> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> > Hello I have only recently started the fmri data analysis and I >> > downloaded freesurfer point by point from martinos site and >> > incorporated the license file as well into the Applications/freesurfer >> > directory. I have run into the first problem and that is of
data
>> > conversion. My file is in dcm format and I have 11,000 dcm
files
to >> > convert. However, before I was using Jamaan Alghamadi created
gui
and >> > it is not able to convert the mri dcm files. Then I shifted to UNIX >> > and again it is saying error. >> > >> > My file is on the desktop and I have given it subject id as
Grace.
My >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> > >> > My terminal look like this before I proceed with the file conversion >> > >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> > >> > dhcp020-223-179:~ sampada$ export >> FREESURFER_HOME=/Applications/freesurfer >> > >> > dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >
>> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>> > >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > >> > FREESURFER_HOME /Applications/freesurfer >> > >> > FSFAST_HOME /Applications/freesurfer/fsfast >> > >> > FSF_OUTPUT_FORMAT nii.gz >> > >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> > >> > MNI_DIR /Applications/freesurfer/mni >> > >> > >> > >> > Will anyone please let me know what I am doing wrong? I will be very >> > grateful for any input. >> > >> > >> > Thanks and regards, >> > >> > >> > Sampada >> > Senior research support specialist >> > Molecular and neuroimaging department >> > Department of Psychiatry >> > 451, biomedical research building >> > University at Buffalo (south campus) >> > Buffalo, NY-14216 >> > >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it >> is >> addressed. If you believe this e-mail was sent to you in error
and
the >> e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent
to
you >> in >> error >> but does not contain patient information, please contact the
sender
and >> properly >> dispose of the e-mail. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all for T1 and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am running this command for recon-all '-all' process. My two files (T1 and T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files .
However,
about the recon-all command do I run it separately for each .mgz file
or
run it one time for all .mgz file(which are eight in numbers)? And
what
command do I use for recon-all? I have tried many but none is
working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I
give
to
free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files
at
one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu > wrote:
> can you send your exact mri_convert commandline? > > > On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > > *Hello freesurfer* > > > > *Sorry for the personal message Shantanu. * > > > > *I managed to convert my dicom to nifti using mricron software, > though > had > > to make some changes to the preferences. * > > > > *About the dcmunpack: The user manual on dcmunpack on fs site
says
> that > > the > > unpackdcmdir is used only to unpack Siemens dicom files. We use > Phillips > > infinity for our PET scan.* > > > > *I am very new to Unix, free surfer and neuroimaging, so
couldn't
> > understand what nipy would do...* > > > > *My FS is working fine as when I typed tkmedit bert orig.mngz
for
> volume > > view it was displaying image.* > > > > *But the when I tried to convert my .nii files to .mgz format ,
I
get
> the > > following error:* > > > > > > Last login: Tue May 6 10:40:32 on ttys000 > > dhcp020-222-117:~ sampada$ export > FREESURFER_HOME=/Applications/freesurfer > > dhcp020-222-117:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > dhcp020-222-117:~ sampada$ mri_convert > > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > > '/Users/sampada/Desktop/test/mri/org/.mgz' > > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii > > /Users/sampada/Desktop/test/mri/org/.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp
$
> > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... > > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (0.0268034, -0.99958, 0.0110098) > > j_ras = (0.0381548, 0.0120287, 0.999199) > > k_ras = (0.998912, 0.0263618, -0.0384612) > > writing to /Users/sampada/Desktop/test/mri/org/.mgz... > > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could
not
> open > > file > > > > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz > > > > > > *Will you please let me know what command I need to use to mri > convert > and > > recon all of my files? * > > I* have 8 .nii files (in the order of
T1>T2>T1>T2>DTI>T1(resting
> stage)>T2 > > (in the order of the acquisition acquired at the time of > experiment).* > > > > > > *Thanks and regards,* > > > > *Sampada* > > > > > > > > > > > > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu > >> wrote: > > > >> > >> Have you tried using dcmunpack? You run it twice, once without
any
> >> output to get a list of runs in the folder. The 2nd with how
you
> want > >> the data converted. Run it with --help to get more info > >> doug > >> > >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > >> > Hello I have only recently started the fmri data analysis
and I
> >> > downloaded freesurfer point by point from martinos site and > >> > incorporated the license file as well into the > Applications/freesurfer > >> > directory. I have run into the first problem and that is of
data
> >> > conversion. My file is in dcm format and I have 11,000 dcm
files
> to > >> > convert. However, before I was using Jamaan Alghamadi
created
gui
> and > >> > it is not able to convert the mri dcm files. Then I shifted
to
> UNIX > >> > and again it is saying error. > >> > > >> > My file is on the desktop and I have given it subject id as
Grace.
> My > >> > directory to the dcm file is '/Users/sampada/desktop/Grace. > >> > > >> > My terminal look like this before I proceed with the file > conversion > >> > > >> > Last login: Mon Apr 28 15:10:13 on ttys001 > >> > > >> > dhcp020-223-179:~ sampada$ export > >> FREESURFER_HOME=/Applications/freesurfer > >> > > >> > dhcp020-223-179:~ sampada$ source > $FREESURFER_HOME/SetUpFreeSurfer.sh > >> > > >> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> -------- > >> > > >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > >> > > >> > FREESURFER_HOME /Applications/freesurfer > >> > > >> > FSFAST_HOME /Applications/freesurfer/fsfast > >> > > >> > FSF_OUTPUT_FORMAT nii.gz > >> > > >> > SUBJECTS_DIR /Applications/freesurfer/subjects > >> > > >> > MNI_DIR /Applications/freesurfer/mni > >> > > >> > > >> > > >> > Will anyone please let me know what I am doing wrong? I will
be
> very > >> > grateful for any input. > >> > > >> > > >> > Thanks and regards, > >> > > >> > > >> > Sampada > >> > Senior research support specialist > >> > Molecular and neuroimaging department > >> > Department of Psychiatry > >> > 451, biomedical research building > >> > University at Buffalo (south campus) > >> > Buffalo, NY-14216 > >> > > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person
to
> whom > >> it > >> is > >> addressed. If you believe this e-mail was sent to you in error
and
> the > >> e-mail > >> contains patient information, please contact the Partners
Compliance
> >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was
sent
to
> you > >> in > >> error > >> but does not contain patient information, please contact the
sender
> and > >> properly > >> dispose of the e-mail. > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger
than
we
> can think. -Werner Heisenberg > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger
than
we
can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all for
T1
and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am running this command for recon-all '-all' process. My two files (T1 and T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files .
However,
about the recon-all command do I run it separately for each .mgz file
or
run it one time for all .mgz file(which are eight in numbers)? And
what
command do I use for recon-all? I have tried many but none is
working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path also, it seems you don't have a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: > Hello Shantanu, > > Many thanks for your reply! This is my exact commandline which I
give
to
> free surfer for the 1st of the eight nii files. When i am able to > convert > this nii to mgz then i will ask how to convert all the eight files
at
> one > go. > > mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > '/Users/sampada/Desktop/test/mri/org/.mgz' > > > Regards, > > Sampada > > > On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh > <shantanu@nmr.mgh.harvard.edu >> wrote: > >> can you send your exact mri_convert commandline? >> >> >> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: >> > *Hello freesurfer* >> > >> > *Sorry for the personal message Shantanu. * >> > >> > *I managed to convert my dicom to nifti using mricron software, >> though >> had >> > to make some changes to the preferences. * >> > >> > *About the dcmunpack: The user manual on dcmunpack on fs site
says
>> that >> > the >> > unpackdcmdir is used only to unpack Siemens dicom files. We use >> Phillips >> > infinity for our PET scan.* >> > >> > *I am very new to Unix, free surfer and neuroimaging, so
couldn't
>> > understand what nipy would do...* >> > >> > *My FS is working fine as when I typed tkmedit bert orig.mngz
for
>> volume >> > view it was displaying image.* >> > >> > *But the when I tried to convert my .nii files to .mgz format ,
I
get
>> the >> > following error:* >> > >> > >> > Last login: Tue May 6 10:40:32 on ttys000 >> > dhcp020-222-117:~ sampada$ export >> FREESURFER_HOME=/Applications/freesurfer >> > dhcp020-222-117:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
>> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> -------- >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > FREESURFER_HOME /Applications/freesurfer >> > FSFAST_HOME /Applications/freesurfer/fsfast >> > FSF_OUTPUT_FORMAT nii.gz >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> > MNI_DIR /Applications/freesurfer/mni >> > dhcp020-222-117:~ sampada$ mri_convert >> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> > '/Users/sampada/Desktop/test/mri/org/.mgz' >> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> > /Users/sampada/Desktop/test/mri/org/.mgz >> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp
$
>> > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... >> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 >> > i_ras = (0.0268034, -0.99958, 0.0110098) >> > j_ras = (0.0381548, 0.0120287, 0.999199) >> > k_ras = (0.998912, 0.0263618, -0.0384612) >> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... >> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could
not
>> open >> > file >> > >> > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz >> > >> > >> > *Will you please let me know what command I need to use to mri >> convert >> and >> > recon all of my files? * >> > I* have 8 .nii files (in the order of
T1>T2>T1>T2>DTI>T1(resting
>> stage)>T2 >> > (in the order of the acquisition acquired at the time of >> experiment).* >> > >> > >> > *Thanks and regards,* >> > >> > *Sampada* >> > >> > >> > >> > >> > >> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve >> > <greve@nmr.mgh.harvard.edu >> >> wrote: >> > >> >> >> >> Have you tried using dcmunpack? You run it twice, once without
any
>> >> output to get a list of runs in the folder. The 2nd with how
you
>> want >> >> the data converted. Run it with --help to get more info >> >> doug >> >> >> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> >> > Hello I have only recently started the fmri data analysis
and I
>> >> > downloaded freesurfer point by point from martinos site and >> >> > incorporated the license file as well into the >> Applications/freesurfer >> >> > directory. I have run into the first problem and that is of
data
>> >> > conversion. My file is in dcm format and I have 11,000 dcm
files
>> to >> >> > convert. However, before I was using Jamaan Alghamadi
created
gui
>> and >> >> > it is not able to convert the mri dcm files. Then I shifted
to
>> UNIX >> >> > and again it is saying error. >> >> > >> >> > My file is on the desktop and I have given it subject id as
Grace.
>> My >> >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> >> > >> >> > My terminal look like this before I proceed with the file >> conversion >> >> > >> >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> >> > >> >> > dhcp020-223-179:~ sampada$ export >> >> FREESURFER_HOME=/Applications/freesurfer >> >> > >> >> > dhcp020-223-179:~ sampada$ source >> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> > >> >> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>> -------- >> >> > >> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >> > >> >> > FREESURFER_HOME /Applications/freesurfer >> >> > >> >> > FSFAST_HOME /Applications/freesurfer/fsfast >> >> > >> >> > FSF_OUTPUT_FORMAT nii.gz >> >> > >> >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >> > >> >> > MNI_DIR /Applications/freesurfer/mni >> >> > >> >> > >> >> > >> >> > Will anyone please let me know what I am doing wrong? I will
be
>> very >> >> > grateful for any input. >> >> > >> >> > >> >> > Thanks and regards, >> >> > >> >> > >> >> > Sampada >> >> > Senior research support specialist >> >> > Molecular and neuroimaging department >> >> > Department of Psychiatry >> >> > 451, biomedical research building >> >> > University at Buffalo (south campus) >> >> > Buffalo, NY-14216 >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> -- >> >> Douglas N. Greve, Ph.D. >> >> MGH-NMR Center >> >> greve@nmr.mgh.harvard.edu >> >> Phone Number: 617-724-2358 >> >> Fax: 617-726-7422 >> >> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> The information in this e-mail is intended only for the person
to
>> whom >> >> it >> >> is >> >> addressed. If you believe this e-mail was sent to you in error
and
>> the >> >> e-mail >> >> contains patient information, please contact the Partners
Compliance
>> >> HelpLine at >> >> http://www.partners.org/complianceline . If the e-mail was
sent
to
>> you >> >> in >> >> error >> >> but does not contain patient information, please contact the
sender
>> and >> >> properly >> >> dispose of the e-mail. >> >> >> >> >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger
than
we
>> can think. -Werner Heisenberg >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger
than
we
can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all
Hth, S.
On Thu, May 15, 2014 2:55 pm, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all
for T1
and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another
subject
and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I
am
running this command for recon-all '-all' process. My two files (T1
and
T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz
and
subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files .
However,
about the recon-all command do I run it separately for each .mgz
file
or
run it one time for all .mgz file(which are eight in numbers)? And
what
command do I use for recon-all? I have tried many but none is
working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
sorry
try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz
Hth, shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > You don't need the quotation marks in your path > also, it seems you don't have a directory called > /Users/sampada/Desktop/test/org > > try something like: > > cd Users/sampada/Desktop/ > mkdir test > cd test > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > sampada/Desktop/test/s400a1001.nii > > Hth, > shantanu > > > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: >> Hello Shantanu, >> >> Many thanks for your reply! This is my exact commandline which
I
give
to >> free surfer for the 1st of the eight nii files. When i am able
to
>> convert >> this nii to mgz then i will ask how to convert all the eight
files
at
>> one >> go. >> >> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >> Regards, >> >> Sampada >> >> >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh >> <shantanu@nmr.mgh.harvard.edu >>> wrote: >> >>> can you send your exact mri_convert commandline? >>> >>> >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: >>> > *Hello freesurfer* >>> > >>> > *Sorry for the personal message Shantanu. * >>> > >>> > *I managed to convert my dicom to nifti using mricron
software,
>>> though >>> had >>> > to make some changes to the preferences. * >>> > >>> > *About the dcmunpack: The user manual on dcmunpack on fs
site
says
>>> that >>> > the >>> > unpackdcmdir is used only to unpack Siemens dicom files. We
use
>>> Phillips >>> > infinity for our PET scan.* >>> > >>> > *I am very new to Unix, free surfer and neuroimaging, so
couldn't
>>> > understand what nipy would do...* >>> > >>> > *My FS is working fine as when I typed tkmedit bert
orig.mngz
for
>>> volume >>> > view it was displaying image.* >>> > >>> > *But the when I tried to convert my .nii files to .mgz
format ,
I
get >>> the >>> > following error:* >>> > >>> > >>> > Last login: Tue May 6 10:40:32 on ttys000 >>> > dhcp020-222-117:~ sampada$ export >>> FREESURFER_HOME=/Applications/freesurfer >>> > dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >>> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>> -------- >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> > FREESURFER_HOME /Applications/freesurfer >>> > FSFAST_HOME /Applications/freesurfer/fsfast >>> > FSF_OUTPUT_FORMAT nii.gz >>> > SUBJECTS_DIR /Applications/freesurfer/subjects >>> > MNI_DIR /Applications/freesurfer/mni >>> > dhcp020-222-117:~ sampada$ mri_convert >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' >>> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii >>> > /Users/sampada/Desktop/test/mri/org/.mgz >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp
$
>>> > reading from
/Users/sampada/Desktop/d2n119495/s400a1001.nii...
>>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 >>> > i_ras = (0.0268034, -0.99958, 0.0110098) >>> > j_ras = (0.0381548, 0.0120287, 0.999199) >>> > k_ras = (0.998912, 0.0263618, -0.0384612) >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1):
could
not
>>> open >>> > file >>> > >>> > ERROR: failure writing
/Users/sampada/Desktop/test/mri/org/.mgz
>>> > >>> > >>> > *Will you please let me know what command I need to use to
mri
>>> convert >>> and >>> > recon all of my files? * >>> > I* have 8 .nii files (in the order of
T1>T2>T1>T2>DTI>T1(resting
>>> stage)>T2 >>> > (in the order of the acquisition acquired at the time of >>> experiment).* >>> > >>> > >>> > *Thanks and regards,* >>> > >>> > *Sampada* >>> > >>> > >>> > >>> > >>> > >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve >>> > <greve@nmr.mgh.harvard.edu >>> >> wrote: >>> > >>> >> >>> >> Have you tried using dcmunpack? You run it twice, once
without
any >>> >> output to get a list of runs in the folder. The 2nd with
how
you
>>> want >>> >> the data converted. Run it with --help to get more info >>> >> doug >>> >> >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >>> >> > Hello I have only recently started the fmri data analysis
and I
>>> >> > downloaded freesurfer point by point from martinos site
and
>>> >> > incorporated the license file as well into the >>> Applications/freesurfer >>> >> > directory. I have run into the first problem and that is
of
data >>> >> > conversion. My file is in dcm format and I have 11,000
dcm
files >>> to >>> >> > convert. However, before I was using Jamaan Alghamadi
created
gui >>> and >>> >> > it is not able to convert the mri dcm files. Then I
shifted
to
>>> UNIX >>> >> > and again it is saying error. >>> >> > >>> >> > My file is on the desktop and I have given it subject id
as
Grace. >>> My >>> >> > directory to the dcm file is
'/Users/sampada/desktop/Grace.
>>> >> > >>> >> > My terminal look like this before I proceed with the file >>> conversion >>> >> > >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 >>> >> > >>> >> > dhcp020-223-179:~ sampada$ export >>> >> FREESURFER_HOME=/Applications/freesurfer >>> >> > >>> >> > dhcp020-223-179:~ sampada$ source >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >>> >> > >>> >> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>> -------- >>> >> > >>> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> >> > >>> >> > FREESURFER_HOME /Applications/freesurfer >>> >> > >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast >>> >> > >>> >> > FSF_OUTPUT_FORMAT nii.gz >>> >> > >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects >>> >> > >>> >> > MNI_DIR /Applications/freesurfer/mni >>> >> > >>> >> > >>> >> > >>> >> > Will anyone please let me know what I am doing wrong? I
will
be
>>> very >>> >> > grateful for any input. >>> >> > >>> >> > >>> >> > Thanks and regards, >>> >> > >>> >> > >>> >> > Sampada >>> >> > Senior research support specialist >>> >> > Molecular and neuroimaging department >>> >> > Department of Psychiatry >>> >> > 451, biomedical research building >>> >> > University at Buffalo (south campus) >>> >> > Buffalo, NY-14216 >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Freesurfer mailing list >>> >> > Freesurfer@nmr.mgh.harvard.edu >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >> >>> >> -- >>> >> Douglas N. Greve, Ph.D. >>> >> MGH-NMR Center >>> >> greve@nmr.mgh.harvard.edu >>> >> Phone Number: 617-724-2358 >>> >> Fax: 617-726-7422 >>> >> >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> >>> >> The information in this e-mail is intended only for the
person
to
>>> whom >>> >> it >>> >> is >>> >> addressed. If you believe this e-mail was sent to you in
error
and >>> the >>> >> e-mail >>> >> contains patient information, please contact the Partners Compliance >>> >> HelpLine at >>> >> http://www.partners.org/complianceline . If the e-mail was
sent
to >>> you >>> >> in >>> >> error >>> >> but does not contain patient information, please contact
the
sender >>> and >>> >> properly >>> >> dispose of the e-mail. >>> >> >>> >> >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Shantanu Ghosh, Ph.D. >>> Harvard Medical School & Massachusetts General Hospital >>> Martinos Center for Biomedical Imaging >>> -- >>> Not only is the universe stranger than we think, it is
stranger
than
we >>> can think. -Werner Heisenberg >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger
than
we > can think. -Werner Heisenberg > >
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger
than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I think the right command needs -s for a subject name (after which a subject folder will be created) and -i for a initial T1 file name.
recon-all -s s600 -i s600a1001.mgz -all
Hope this helps! Markus
2014-05-15 23:23 GMT+02:00 Shantanu Ghosh shantanu@nmr.mgh.harvard.edu:
remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all
Hth, S.
On Thu, May 15, 2014 2:55 pm, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp:
/Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt:
Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all
for T1
and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another
subject
and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I
am
running this command for recon-all '-all' process. My two files (T1
and
T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz
and
subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files .
However,
about the recon-all command do I run it separately for each .mgz
file
or
run it one time for all .mgz file(which are eight in numbers)? And
what
command do I use for recon-all? I have tried many but none is
working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
> sorry > > try: > > cd Users/sampada/Desktop/ > mkdir test > cd test > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > sampada/Desktop/test/s400a1001.mgz > > Hth, > shantanu > > On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > > You don't need the quotation marks in your path > > also, it seems you don't have a directory called > > /Users/sampada/Desktop/test/org > > > > try something like: > > > > cd Users/sampada/Desktop/ > > mkdir test > > cd test > > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > > sampada/Desktop/test/s400a1001.nii > > > > Hth, > > shantanu > > > > > > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: > >> Hello Shantanu, > >> > >> Many thanks for your reply! This is my exact commandline which
I
give
> to > >> free surfer for the 1st of the eight nii files. When i am able
to
> >> convert > >> this nii to mgz then i will ask how to convert all the eight
files
at
> >> one > >> go. > >> > >> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > >> '/Users/sampada/Desktop/test/mri/org/.mgz' > >> > >> > >> Regards, > >> > >> Sampada > >> > >> > >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh > >> <shantanu@nmr.mgh.harvard.edu > >>> wrote: > >> > >>> can you send your exact mri_convert commandline? > >>> > >>> > >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > >>> > *Hello freesurfer* > >>> > > >>> > *Sorry for the personal message Shantanu. * > >>> > > >>> > *I managed to convert my dicom to nifti using mricron
software,
> >>> though > >>> had > >>> > to make some changes to the preferences. * > >>> > > >>> > *About the dcmunpack: The user manual on dcmunpack on fs
site
says
> >>> that > >>> > the > >>> > unpackdcmdir is used only to unpack Siemens dicom files. We
use
> >>> Phillips > >>> > infinity for our PET scan.* > >>> > > >>> > *I am very new to Unix, free surfer and neuroimaging, so
couldn't
> >>> > understand what nipy would do...* > >>> > > >>> > *My FS is working fine as when I typed tkmedit bert
orig.mngz
for
> >>> volume > >>> > view it was displaying image.* > >>> > > >>> > *But the when I tried to convert my .nii files to .mgz
format ,
I
> get > >>> the > >>> > following error:* > >>> > > >>> > > >>> > Last login: Tue May 6 10:40:32 on ttys000 > >>> > dhcp020-222-117:~ sampada$ export > >>> FREESURFER_HOME=/Applications/freesurfer > >>> > dhcp020-222-117:~ sampada$ source > $FREESURFER_HOME/SetUpFreeSurfer.sh > >>> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> >>> -------- > >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > >>> > FREESURFER_HOME /Applications/freesurfer > >>> > FSFAST_HOME /Applications/freesurfer/fsfast > >>> > FSF_OUTPUT_FORMAT nii.gz > >>> > SUBJECTS_DIR /Applications/freesurfer/subjects > >>> > MNI_DIR /Applications/freesurfer/mni > >>> > dhcp020-222-117:~ sampada$ mri_convert > >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' > >>> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii > >>> > /Users/sampada/Desktop/test/mri/org/.mgz > >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp
$
> >>> > reading from
/Users/sampada/Desktop/d2n119495/s400a1001.nii...
> >>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 > >>> > i_ras = (0.0268034, -0.99958, 0.0110098) > >>> > j_ras = (0.0381548, 0.0120287, 0.999199) > >>> > k_ras = (0.998912, 0.0263618, -0.0384612) > >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... > >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1):
could
not
> >>> open > >>> > file > >>> > > >>> > ERROR: failure writing
/Users/sampada/Desktop/test/mri/org/.mgz
> >>> > > >>> > > >>> > *Will you please let me know what command I need to use to
mri
> >>> convert > >>> and > >>> > recon all of my files? * > >>> > I* have 8 .nii files (in the order of
T1>T2>T1>T2>DTI>T1(resting
> >>> stage)>T2 > >>> > (in the order of the acquisition acquired at the time of > >>> experiment).* > >>> > > >>> > > >>> > *Thanks and regards,* > >>> > > >>> > *Sampada* > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu > >>> >> wrote: > >>> > > >>> >> > >>> >> Have you tried using dcmunpack? You run it twice, once
without
> any > >>> >> output to get a list of runs in the folder. The 2nd with
how
you
> >>> want > >>> >> the data converted. Run it with --help to get more info > >>> >> doug > >>> >> > >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > >>> >> > Hello I have only recently started the fmri data analysis
and I
> >>> >> > downloaded freesurfer point by point from martinos site
and
> >>> >> > incorporated the license file as well into the > >>> Applications/freesurfer > >>> >> > directory. I have run into the first problem and that is
of
> data > >>> >> > conversion. My file is in dcm format and I have 11,000
dcm
> files > >>> to > >>> >> > convert. However, before I was using Jamaan Alghamadi
created
> gui > >>> and > >>> >> > it is not able to convert the mri dcm files. Then I
shifted
to
> >>> UNIX > >>> >> > and again it is saying error. > >>> >> > > >>> >> > My file is on the desktop and I have given it subject id
as
> Grace. > >>> My > >>> >> > directory to the dcm file is
'/Users/sampada/desktop/Grace.
> >>> >> > > >>> >> > My terminal look like this before I proceed with the file > >>> conversion > >>> >> > > >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 > >>> >> > > >>> >> > dhcp020-223-179:~ sampada$ export > >>> >> FREESURFER_HOME=/Applications/freesurfer > >>> >> > > >>> >> > dhcp020-223-179:~ sampada$ source > >>> $FREESURFER_HOME/SetUpFreeSurfer.sh > >>> >> > > >>> >> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> >>> -------- > >>> >> > > >>> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > >>> >> > > >>> >> > FREESURFER_HOME /Applications/freesurfer > >>> >> > > >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast > >>> >> > > >>> >> > FSF_OUTPUT_FORMAT nii.gz > >>> >> > > >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects > >>> >> > > >>> >> > MNI_DIR /Applications/freesurfer/mni > >>> >> > > >>> >> > > >>> >> > > >>> >> > Will anyone please let me know what I am doing wrong? I
will
be
> >>> very > >>> >> > grateful for any input. > >>> >> > > >>> >> > > >>> >> > Thanks and regards, > >>> >> > > >>> >> > > >>> >> > Sampada > >>> >> > Senior research support specialist > >>> >> > Molecular and neuroimaging department > >>> >> > Department of Psychiatry > >>> >> > 451, biomedical research building > >>> >> > University at Buffalo (south campus) > >>> >> > Buffalo, NY-14216 > >>> >> > > >>> >> > > >>> >> > > >>> >> > > >>> >> > > >>> >> > _______________________________________________ > >>> >> > Freesurfer mailing list > >>> >> > Freesurfer@nmr.mgh.harvard.edu > >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >> > >>> >> -- > >>> >> Douglas N. Greve, Ph.D. > >>> >> MGH-NMR Center > >>> >> greve@nmr.mgh.harvard.edu > >>> >> Phone Number: 617-724-2358 > >>> >> Fax: 617-726-7422 > >>> >> > >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> >> Outgoing: > >>>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu > >>> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >> > >>> >> > >>> >> The information in this e-mail is intended only for the
person
to
> >>> whom > >>> >> it > >>> >> is > >>> >> addressed. If you believe this e-mail was sent to you in
error
> and > >>> the > >>> >> e-mail > >>> >> contains patient information, please contact the Partners > Compliance > >>> >> HelpLine at > >>> >> http://www.partners.org/complianceline . If the e-mail was
sent
> to > >>> you > >>> >> in > >>> >> error > >>> >> but does not contain patient information, please contact
the
> sender > >>> and > >>> >> properly > >>> >> dispose of the e-mail. > >>> >> > >>> >> > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu > >>> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> > >>> > >>> -- > >>> Shantanu Ghosh, Ph.D. > >>> Harvard Medical School & Massachusetts General Hospital > >>> Martinos Center for Biomedical Imaging > >>> -- > >>> Not only is the universe stranger than we think, it is
stranger
than
> we > >>> can think. -Werner Heisenberg > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Shantanu Ghosh, Ph.D. > > Harvard Medical School & Massachusetts General Hospital > > Martinos Center for Biomedical Imaging > > -- > > Not only is the universe stranger than we think, it is stranger
than
> we > > can think. -Werner Heisenberg > > > > > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger
than
we
> can think. -Werner Heisenberg > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Shantanu,
Thanks for your mail, but the error is still the same:
Last login: Thu May 15 17:31:29 on ttys000 dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd /Users/sampada/Desktop/Vaibhav2/ dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz -all mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Since my file s600a1001.mgz is not a directory, do I need to make an intermediate directory for the recon all process to run?
Thanks and regards,
Sampada
On Thu, May 15, 2014 at 5:23 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all
Hth, S.
On Thu, May 15, 2014 2:55 pm, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp:
/Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt:
Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all
for T1
and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another
subject
and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I
am
running this command for recon-all '-all' process. My two files (T1
and
T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz
and
subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the structural T1 dataset. After that you can use the tutorials from the freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files .
However,
about the recon-all command do I run it separately for each .mgz
file
or
run it one time for all .mgz file(which are eight in numbers)? And
what
command do I use for recon-all? I have tried many but none is
working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
> sorry > > try: > > cd Users/sampada/Desktop/ > mkdir test > cd test > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > sampada/Desktop/test/s400a1001.mgz > > Hth, > shantanu > > On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > > You don't need the quotation marks in your path > > also, it seems you don't have a directory called > > /Users/sampada/Desktop/test/org > > > > try something like: > > > > cd Users/sampada/Desktop/ > > mkdir test > > cd test > > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > > sampada/Desktop/test/s400a1001.nii > > > > Hth, > > shantanu > > > > > > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: > >> Hello Shantanu, > >> > >> Many thanks for your reply! This is my exact commandline which
I
give
> to > >> free surfer for the 1st of the eight nii files. When i am able
to
> >> convert > >> this nii to mgz then i will ask how to convert all the eight
files
at
> >> one > >> go. > >> > >> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > >> '/Users/sampada/Desktop/test/mri/org/.mgz' > >> > >> > >> Regards, > >> > >> Sampada > >> > >> > >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh > >> <shantanu@nmr.mgh.harvard.edu > >>> wrote: > >> > >>> can you send your exact mri_convert commandline? > >>> > >>> > >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > >>> > *Hello freesurfer* > >>> > > >>> > *Sorry for the personal message Shantanu. * > >>> > > >>> > *I managed to convert my dicom to nifti using mricron
software,
> >>> though > >>> had > >>> > to make some changes to the preferences. * > >>> > > >>> > *About the dcmunpack: The user manual on dcmunpack on fs
site
says
> >>> that > >>> > the > >>> > unpackdcmdir is used only to unpack Siemens dicom files. We
use
> >>> Phillips > >>> > infinity for our PET scan.* > >>> > > >>> > *I am very new to Unix, free surfer and neuroimaging, so
couldn't
> >>> > understand what nipy would do...* > >>> > > >>> > *My FS is working fine as when I typed tkmedit bert
orig.mngz
for
> >>> volume > >>> > view it was displaying image.* > >>> > > >>> > *But the when I tried to convert my .nii files to .mgz
format ,
I
> get > >>> the > >>> > following error:* > >>> > > >>> > > >>> > Last login: Tue May 6 10:40:32 on ttys000 > >>> > dhcp020-222-117:~ sampada$ export > >>> FREESURFER_HOME=/Applications/freesurfer > >>> > dhcp020-222-117:~ sampada$ source > $FREESURFER_HOME/SetUpFreeSurfer.sh > >>> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> >>> -------- > >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > >>> > FREESURFER_HOME /Applications/freesurfer > >>> > FSFAST_HOME /Applications/freesurfer/fsfast > >>> > FSF_OUTPUT_FORMAT nii.gz > >>> > SUBJECTS_DIR /Applications/freesurfer/subjects > >>> > MNI_DIR /Applications/freesurfer/mni > >>> > dhcp020-222-117:~ sampada$ mri_convert > >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' > >>> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii > >>> > /Users/sampada/Desktop/test/mri/org/.mgz > >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp
$
> >>> > reading from
/Users/sampada/Desktop/d2n119495/s400a1001.nii...
> >>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 > >>> > i_ras = (0.0268034, -0.99958, 0.0110098) > >>> > j_ras = (0.0381548, 0.0120287, 0.999199) > >>> > k_ras = (0.998912, 0.0263618, -0.0384612) > >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... > >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1):
could
not
> >>> open > >>> > file > >>> > > >>> > ERROR: failure writing
/Users/sampada/Desktop/test/mri/org/.mgz
> >>> > > >>> > > >>> > *Will you please let me know what command I need to use to
mri
> >>> convert > >>> and > >>> > recon all of my files? * > >>> > I* have 8 .nii files (in the order of
T1>T2>T1>T2>DTI>T1(resting
> >>> stage)>T2 > >>> > (in the order of the acquisition acquired at the time of > >>> experiment).* > >>> > > >>> > > >>> > *Thanks and regards,* > >>> > > >>> > *Sampada* > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu > >>> >> wrote: > >>> > > >>> >> > >>> >> Have you tried using dcmunpack? You run it twice, once
without
> any > >>> >> output to get a list of runs in the folder. The 2nd with
how
you
> >>> want > >>> >> the data converted. Run it with --help to get more info > >>> >> doug > >>> >> > >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > >>> >> > Hello I have only recently started the fmri data analysis
and I
> >>> >> > downloaded freesurfer point by point from martinos site
and
> >>> >> > incorporated the license file as well into the > >>> Applications/freesurfer > >>> >> > directory. I have run into the first problem and that is
of
> data > >>> >> > conversion. My file is in dcm format and I have 11,000
dcm
> files > >>> to > >>> >> > convert. However, before I was using Jamaan Alghamadi
created
> gui > >>> and > >>> >> > it is not able to convert the mri dcm files. Then I
shifted
to
> >>> UNIX > >>> >> > and again it is saying error. > >>> >> > > >>> >> > My file is on the desktop and I have given it subject id
as
> Grace. > >>> My > >>> >> > directory to the dcm file is
'/Users/sampada/desktop/Grace.
> >>> >> > > >>> >> > My terminal look like this before I proceed with the file > >>> conversion > >>> >> > > >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 > >>> >> > > >>> >> > dhcp020-223-179:~ sampada$ export > >>> >> FREESURFER_HOME=/Applications/freesurfer > >>> >> > > >>> >> > dhcp020-223-179:~ sampada$ source > >>> $FREESURFER_HOME/SetUpFreeSurfer.sh > >>> >> > > >>> >> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> >>> -------- > >>> >> > > >>> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > >>> >> > > >>> >> > FREESURFER_HOME /Applications/freesurfer > >>> >> > > >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast > >>> >> > > >>> >> > FSF_OUTPUT_FORMAT nii.gz > >>> >> > > >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects > >>> >> > > >>> >> > MNI_DIR /Applications/freesurfer/mni > >>> >> > > >>> >> > > >>> >> > > >>> >> > Will anyone please let me know what I am doing wrong? I
will
be
> >>> very > >>> >> > grateful for any input. > >>> >> > > >>> >> > > >>> >> > Thanks and regards, > >>> >> > > >>> >> > > >>> >> > Sampada > >>> >> > Senior research support specialist > >>> >> > Molecular and neuroimaging department > >>> >> > Department of Psychiatry > >>> >> > 451, biomedical research building > >>> >> > University at Buffalo (south campus) > >>> >> > Buffalo, NY-14216 > >>> >> > > >>> >> > > >>> >> > > >>> >> > > >>> >> > > >>> >> > _______________________________________________ > >>> >> > Freesurfer mailing list > >>> >> > Freesurfer@nmr.mgh.harvard.edu > >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >> > >>> >> -- > >>> >> Douglas N. Greve, Ph.D. > >>> >> MGH-NMR Center > >>> >> greve@nmr.mgh.harvard.edu > >>> >> Phone Number: 617-724-2358 > >>> >> Fax: 617-726-7422 > >>> >> > >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> >> Outgoing: > >>>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu > >>> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >> > >>> >> > >>> >> The information in this e-mail is intended only for the
person
to
> >>> whom > >>> >> it > >>> >> is > >>> >> addressed. If you believe this e-mail was sent to you in
error
> and > >>> the > >>> >> e-mail > >>> >> contains patient information, please contact the Partners > Compliance > >>> >> HelpLine at > >>> >> http://www.partners.org/complianceline . If the e-mail was
sent
> to > >>> you > >>> >> in > >>> >> error > >>> >> but does not contain patient information, please contact
the
> sender > >>> and > >>> >> properly > >>> >> dispose of the e-mail. > >>> >> > >>> >> > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu > >>> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> > >>> > >>> -- > >>> Shantanu Ghosh, Ph.D. > >>> Harvard Medical School & Massachusetts General Hospital > >>> Martinos Center for Biomedical Imaging > >>> -- > >>> Not only is the universe stranger than we think, it is
stranger
than
> we > >>> can think. -Werner Heisenberg > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Shantanu Ghosh, Ph.D. > > Harvard Medical School & Massachusetts General Hospital > > Martinos Center for Biomedical Imaging > > -- > > Not only is the universe stranger than we think, it is stranger
than
> we > > can think. -Werner Heisenberg > > > > > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger
than
we
> can think. -Werner Heisenberg > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
You are using with the extension .mgz thats wrong try: recon-all -s s600a1001 -all
and as Markus suggests, use the -s flag for the subject directory
Hth, Es
On Thu, May 15, 2014 6:00 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Thanks for your mail, but the error is still the same:
Last login: Thu May 15 17:31:29 on ttys000 dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd /Users/sampada/Desktop/Vaibhav2/ dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz -all mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Since my file s600a1001.mgz is not a directory, do I need to make an intermediate directory for the recon all process to run?
Thanks and regards,
Sampada
On Thu, May 15, 2014 at 5:23 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all
Hth, S.
On Thu, May 15, 2014 2:55 pm, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this
command
and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp:
/Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt:
Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all
the
subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current
one
with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer, thanks for your message. I am doing the recon-all
for T1
and T2* structural dataset now I have in all 8 files in the order
of
(T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another
subject
and we have one T1 file s600a1001.mgz. Since my shell is a bash shell,
I
am
running this command for recon-all '-all' process. My two files (T1
and
T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz
and
subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-041:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2
dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all'
ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz
Even when I make the intermediate directory of mri/orig, its still
not
recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on
the
structural T1 dataset. After that you can use the tutorials from
the
freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki)
Hth, Shantanu
On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote: > Hello Freesurfer, > > Thanks Shantanu I was able to convert the .nii to .mgz files . However, > about the recon-all command do I run it separately for each .mgz
file
or > run it one time for all .mgz file(which are eight in numbers)?
And
what > command do I use for recon-all? I have tried many but none is working.. > > Thanks and regards, > > Sampada > > > > > > > On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < > shantanu@nmr.mgh.harvard.edu> wrote: > >> sorry >> >> try: >> >> cd Users/sampada/Desktop/ >> mkdir test >> cd test >> mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> sampada/Desktop/test/s400a1001.mgz >> >> Hth, >> shantanu >> >> On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: >> > You don't need the quotation marks in your path >> > also, it seems you don't have a directory called >> > /Users/sampada/Desktop/test/org >> > >> > try something like: >> > >> > cd Users/sampada/Desktop/ >> > mkdir test >> > cd test >> > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> > sampada/Desktop/test/s400a1001.nii >> > >> > Hth, >> > shantanu >> > >> > >> > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: >> >> Hello Shantanu, >> >> >> >> Many thanks for your reply! This is my exact commandline
which
I
give >> to >> >> free surfer for the 1st of the eight nii files. When i am
able
to
>> >> convert >> >> this nii to mgz then i will ask how to convert all the eight
files
at >> >> one >> >> go. >> >> >> >> mri_convert
'/Users/sampada/Desktop/d2n119495/s400a1001.nii'
>> >> '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >> >> >> >> Regards, >> >> >> >> Sampada >> >> >> >> >> >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh >> >> <shantanu@nmr.mgh.harvard.edu >> >>> wrote: >> >> >> >>> can you send your exact mri_convert commandline? >> >>> >> >>> >> >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: >> >>> > *Hello freesurfer* >> >>> > >> >>> > *Sorry for the personal message Shantanu. * >> >>> > >> >>> > *I managed to convert my dicom to nifti using mricron
software,
>> >>> though >> >>> had >> >>> > to make some changes to the preferences. * >> >>> > >> >>> > *About the dcmunpack: The user manual on dcmunpack on fs
site
says >> >>> that >> >>> > the >> >>> > unpackdcmdir is used only to unpack Siemens dicom files.
We
use
>> >>> Phillips >> >>> > infinity for our PET scan.* >> >>> > >> >>> > *I am very new to Unix, free surfer and neuroimaging, so couldn't >> >>> > understand what nipy would do...* >> >>> > >> >>> > *My FS is working fine as when I typed tkmedit bert
orig.mngz
for >> >>> volume >> >>> > view it was displaying image.* >> >>> > >> >>> > *But the when I tried to convert my .nii files to .mgz
format ,
I >> get >> >>> the >> >>> > following error:* >> >>> > >> >>> > >> >>> > Last login: Tue May 6 10:40:32 on ttys000 >> >>> > dhcp020-222-117:~ sampada$ export >> >>> FREESURFER_HOME=/Applications/freesurfer >> >>> > dhcp020-222-117:~ sampada$ source >> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >>> > --------
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>> >>> -------- >> >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >>> > FREESURFER_HOME /Applications/freesurfer >> >>> > FSFAST_HOME /Applications/freesurfer/fsfast >> >>> > FSF_OUTPUT_FORMAT nii.gz >> >>> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >>> > MNI_DIR /Applications/freesurfer/mni >> >>> > dhcp020-222-117:~ sampada$ mri_convert >> >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' >> >>> > mri_convert
/Users/sampada/Desktop/d2n119495/s400a1001.nii
>> >>> > /Users/sampada/Desktop/test/mri/org/.mgz >> >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp
$ >> >>> > reading from
/Users/sampada/Desktop/d2n119495/s400a1001.nii...
>> >>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 >> >>> > i_ras = (0.0268034, -0.99958, 0.0110098) >> >>> > j_ras = (0.0381548, 0.0120287, 0.999199) >> >>> > k_ras = (0.998912, 0.0263618, -0.0384612) >> >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... >> >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1):
could
not >> >>> open >> >>> > file >> >>> > >> >>> > ERROR: failure writing
/Users/sampada/Desktop/test/mri/org/.mgz
>> >>> > >> >>> > >> >>> > *Will you please let me know what command I need to use
to
mri
>> >>> convert >> >>> and >> >>> > recon all of my files? * >> >>> > I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting >> >>> stage)>T2 >> >>> > (in the order of the acquisition acquired at the time of >> >>> experiment).* >> >>> > >> >>> > >> >>> > *Thanks and regards,* >> >>> > >> >>> > *Sampada* >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve >> >>> > <greve@nmr.mgh.harvard.edu >> >>> >> wrote: >> >>> > >> >>> >> >> >>> >> Have you tried using dcmunpack? You run it twice, once
without
>> any >> >>> >> output to get a list of runs in the folder. The 2nd with
how
you >> >>> want >> >>> >> the data converted. Run it with --help to get more info >> >>> >> doug >> >>> >> >> >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> >>> >> > Hello I have only recently started the fmri data
analysis
and I >> >>> >> > downloaded freesurfer point by point from martinos
site
and
>> >>> >> > incorporated the license file as well into the >> >>> Applications/freesurfer >> >>> >> > directory. I have run into the first problem and that
is
of
>> data >> >>> >> > conversion. My file is in dcm format and I have 11,000
dcm
>> files >> >>> to >> >>> >> > convert. However, before I was using Jamaan Alghamadi created >> gui >> >>> and >> >>> >> > it is not able to convert the mri dcm files. Then I
shifted
to >> >>> UNIX >> >>> >> > and again it is saying error. >> >>> >> > >> >>> >> > My file is on the desktop and I have given it subject
id
as
>> Grace. >> >>> My >> >>> >> > directory to the dcm file is
'/Users/sampada/desktop/Grace.
>> >>> >> > >> >>> >> > My terminal look like this before I proceed with the
file
>> >>> conversion >> >>> >> > >> >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> >>> >> > >> >>> >> > dhcp020-223-179:~ sampada$ export >> >>> >> FREESURFER_HOME=/Applications/freesurfer >> >>> >> > >> >>> >> > dhcp020-223-179:~ sampada$ source >> >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >>> >> > >> >>> >> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >>> -------- >> >>> >> > >> >>> >> > Setting up environment for FreeSurfer/FS-FAST (and
FSL)
>> >>> >> > >> >>> >> > FREESURFER_HOME /Applications/freesurfer >> >>> >> > >> >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast >> >>> >> > >> >>> >> > FSF_OUTPUT_FORMAT nii.gz >> >>> >> > >> >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >>> >> > >> >>> >> > MNI_DIR /Applications/freesurfer/mni >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > Will anyone please let me know what I am doing wrong?
I
will
be >> >>> very >> >>> >> > grateful for any input. >> >>> >> > >> >>> >> > >> >>> >> > Thanks and regards, >> >>> >> > >> >>> >> > >> >>> >> > Sampada >> >>> >> > Senior research support specialist >> >>> >> > Molecular and neuroimaging department >> >>> >> > Department of Psychiatry >> >>> >> > 451, biomedical research building >> >>> >> > University at Buffalo (south campus) >> >>> >> > Buffalo, NY-14216 >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > _______________________________________________ >> >>> >> > Freesurfer mailing list >> >>> >> > Freesurfer@nmr.mgh.harvard.edu >> >>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>> >> >> >>> >> -- >> >>> >> Douglas N. Greve, Ph.D. >> >>> >> MGH-NMR Center >> >>> >> greve@nmr.mgh.harvard.edu >> >>> >> Phone Number: 617-724-2358 >> >>> >> Fax: 617-726-7422 >> >>> >> >> >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >>> >> Outgoing: >> >>>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >>> >> >> >>> >> _______________________________________________ >> >>> >> Freesurfer mailing list >> >>> >> Freesurfer@nmr.mgh.harvard.edu >> >>> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>> >> >> >>> >> >> >>> >> The information in this e-mail is intended only for the
person
to >> >>> whom >> >>> >> it >> >>> >> is >> >>> >> addressed. If you believe this e-mail was sent to you in
error
>> and >> >>> the >> >>> >> e-mail >> >>> >> contains patient information, please contact the
Partners
>> Compliance >> >>> >> HelpLine at >> >>> >> http://www.partners.org/complianceline . If the e-mail
was
sent >> to >> >>> you >> >>> >> in >> >>> >> error >> >>> >> but does not contain patient information, please contact
the
>> sender >> >>> and >> >>> >> properly >> >>> >> dispose of the e-mail. >> >>> >> >> >>> >> >> >>> > _______________________________________________ >> >>> > Freesurfer mailing list >> >>> > Freesurfer@nmr.mgh.harvard.edu >> >>> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>> >> >>> >> >>> -- >> >>> Shantanu Ghosh, Ph.D. >> >>> Harvard Medical School & Massachusetts General Hospital >> >>> Martinos Center for Biomedical Imaging >> >>> -- >> >>> Not only is the universe stranger than we think, it is
stranger
than >> we >> >>> can think. -Werner Heisenberg >> >>> >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer@nmr.mgh.harvard.edu >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > -- >> > Shantanu Ghosh, Ph.D. >> > Harvard Medical School & Massachusetts General Hospital >> > Martinos Center for Biomedical Imaging >> > -- >> > Not only is the universe stranger than we think, it is
stranger
than >> we >> > can think. -Werner Heisenberg >> > >> > >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger
than
we >> can think. -Werner Heisenberg >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger
than
we
can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than
we
can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Use something like
recon-all -s s600a1001 -i s600a1001.mgz -all
On 05/15/2014 02:55 PM, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu mailto:shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/ and then run recon-all S. On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote: > Hello freesurfer, thanks for your message. I am doing the recon-all for T1 > and T2* structural dataset now I have in all 8 files in the order of > (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject > and > we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am > running this command for recon-all '-all' process. My two files (T1 and > T2*) are in the Vaibhav2 folder. > My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and > subject id is s600a1001.mgz > > sampada$ export FREESURFER_HOME=/Applications/freesurfer > > dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2 > > dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' > > ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz > > > Even when I make the intermediate directory of mri/orig, its still not > recognising the command and shows an error. > > > Thanks and regards, > > > Sampada > > > > On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh > <shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu> >> wrote: > >> You should try to run recon_all command with -all flag to run on the >> structural T1 dataset. After that you can use the tutorials from the >> freesurfer wiki to do a Feat analysis. >> >> For recon_all you need to specify only the subject and the script >> automatically does the rest. Segmentation and parcellation is >> automatized >> (see wiki) >> >> Hth, >> Shantanu >> >> >> On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote: >> > Hello Freesurfer, >> > >> > Thanks Shantanu I was able to convert the .nii to .mgz files . >> However, >> > about the recon-all command do I run it separately for each .mgz file >> or >> > run it one time for all .mgz file(which are eight in numbers)? And >> what >> > command do I use for recon-all? I have tried many but none is >> working.. >> > >> > Thanks and regards, >> > >> > Sampada >> > >> > >> > >> > >> > >> > >> > On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < >> > shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu>> wrote: >> > >> >> sorry >> >> >> >> try: >> >> >> >> cd Users/sampada/Desktop/ >> >> mkdir test >> >> cd test >> >> mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> >> sampada/Desktop/test/s400a1001.mgz >> >> >> >> Hth, >> >> shantanu >> >> >> >> On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: >> >> > You don't need the quotation marks in your path >> >> > also, it seems you don't have a directory called >> >> > /Users/sampada/Desktop/test/org >> >> > >> >> > try something like: >> >> > >> >> > cd Users/sampada/Desktop/ >> >> > mkdir test >> >> > cd test >> >> > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> >> > sampada/Desktop/test/s400a1001.nii >> >> > >> >> > Hth, >> >> > shantanu >> >> > >> >> > >> >> > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: >> >> >> Hello Shantanu, >> >> >> >> >> >> Many thanks for your reply! This is my exact commandline which I >> give >> >> to >> >> >> free surfer for the 1st of the eight nii files. When i am able to >> >> >> convert >> >> >> this nii to mgz then i will ask how to convert all the eight files >> at >> >> >> one >> >> >> go. >> >> >> >> >> >> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> >> >> '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >> >> >> >> >> >> >> Regards, >> >> >> >> >> >> Sampada >> >> >> >> >> >> >> >> >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh >> >> >> <shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu> >> >> >>> wrote: >> >> >> >> >> >>> can you send your exact mri_convert commandline? >> >> >>> >> >> >>> >> >> >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: >> >> >>> > *Hello freesurfer* >> >> >>> > >> >> >>> > *Sorry for the personal message Shantanu. * >> >> >>> > >> >> >>> > *I managed to convert my dicom to nifti using mricron software, >> >> >>> though >> >> >>> had >> >> >>> > to make some changes to the preferences. * >> >> >>> > >> >> >>> > *About the dcmunpack: The user manual on dcmunpack on fs site >> says >> >> >>> that >> >> >>> > the >> >> >>> > unpackdcmdir is used only to unpack Siemens dicom files. We use >> >> >>> Phillips >> >> >>> > infinity for our PET scan.* >> >> >>> > >> >> >>> > *I am very new to Unix, free surfer and neuroimaging, so >> couldn't >> >> >>> > understand what nipy would do...* >> >> >>> > >> >> >>> > *My FS is working fine as when I typed tkmedit bert orig.mngz >> for >> >> >>> volume >> >> >>> > view it was displaying image.* >> >> >>> > >> >> >>> > *But the when I tried to convert my .nii files to .mgz format , >> I >> >> get >> >> >>> the >> >> >>> > following error:* >> >> >>> > >> >> >>> > >> >> >>> > Last login: Tue May 6 10:40:32 on ttys000 >> >> >>> > dhcp020-222-117:~ sampada$ export >> >> >>> FREESURFER_HOME=/Applications/freesurfer >> >> >>> > dhcp020-222-117:~ sampada$ source >> >> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >>> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >> >>> -------- >> >> >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >> >>> > FREESURFER_HOME /Applications/freesurfer >> >> >>> > FSFAST_HOME /Applications/freesurfer/fsfast >> >> >>> > FSF_OUTPUT_FORMAT nii.gz >> >> >>> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >> >>> > MNI_DIR /Applications/freesurfer/mni >> >> >>> > dhcp020-222-117:~ sampada$ mri_convert >> >> >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> >> >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >>> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> >> >>> > /Users/sampada/Desktop/test/mri/org/.mgz >> >> >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp >> $ >> >> >>> > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... >> >> >>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 >> >> >>> > i_ras = (0.0268034, -0.99958, 0.0110098) >> >> >>> > j_ras = (0.0381548, 0.0120287, 0.999199) >> >> >>> > k_ras = (0.998912, 0.0263618, -0.0384612) >> >> >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... >> >> >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could >> not >> >> >>> open >> >> >>> > file >> >> >>> > >> >> >>> > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz >> >> >>> > >> >> >>> > >> >> >>> > *Will you please let me know what command I need to use to mri >> >> >>> convert >> >> >>> and >> >> >>> > recon all of my files? * >> >> >>> > I* have 8 .nii files (in the order of >> T1>T2>T1>T2>DTI>T1(resting >> >> >>> stage)>T2 >> >> >>> > (in the order of the acquisition acquired at the time of >> >> >>> experiment).* >> >> >>> > >> >> >>> > >> >> >>> > *Thanks and regards,* >> >> >>> > >> >> >>> > *Sampada* >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve >> >> >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> >> >>> >> wrote: >> >> >>> > >> >> >>> >> >> >> >>> >> Have you tried using dcmunpack? You run it twice, once without >> >> any >> >> >>> >> output to get a list of runs in the folder. The 2nd with how >> you >> >> >>> want >> >> >>> >> the data converted. Run it with --help to get more info >> >> >>> >> doug >> >> >>> >> >> >> >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> >> >>> >> > Hello I have only recently started the fmri data analysis >> and I >> >> >>> >> > downloaded freesurfer point by point from martinos site and >> >> >>> >> > incorporated the license file as well into the >> >> >>> Applications/freesurfer >> >> >>> >> > directory. I have run into the first problem and that is of >> >> data >> >> >>> >> > conversion. My file is in dcm format and I have 11,000 dcm >> >> files >> >> >>> to >> >> >>> >> > convert. However, before I was using Jamaan Alghamadi >> created >> >> gui >> >> >>> and >> >> >>> >> > it is not able to convert the mri dcm files. Then I shifted >> to >> >> >>> UNIX >> >> >>> >> > and again it is saying error. >> >> >>> >> > >> >> >>> >> > My file is on the desktop and I have given it subject id as >> >> Grace. >> >> >>> My >> >> >>> >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> >> >>> >> > >> >> >>> >> > My terminal look like this before I proceed with the file >> >> >>> conversion >> >> >>> >> > >> >> >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> >> >>> >> > >> >> >>> >> > dhcp020-223-179:~ sampada$ export >> >> >>> >> FREESURFER_HOME=/Applications/freesurfer >> >> >>> >> > >> >> >>> >> > dhcp020-223-179:~ sampada$ source >> >> >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >>> >> > >> >> >>> >> > -------- >> freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >> >>> -------- >> >> >>> >> > >> >> >>> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >> >>> >> > >> >> >>> >> > FREESURFER_HOME /Applications/freesurfer >> >> >>> >> > >> >> >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast >> >> >>> >> > >> >> >>> >> > FSF_OUTPUT_FORMAT nii.gz >> >> >>> >> > >> >> >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >> >>> >> > >> >> >>> >> > MNI_DIR /Applications/freesurfer/mni >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Will anyone please let me know what I am doing wrong? I will >> be >> >> >>> very >> >> >>> >> > grateful for any input. >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Thanks and regards, >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Sampada >> >> >>> >> > Senior research support specialist >> >> >>> >> > Molecular and neuroimaging department >> >> >>> >> > Department of Psychiatry >> >> >>> >> > 451, biomedical research building >> >> >>> >> > University at Buffalo (south campus) >> >> >>> >> > Buffalo, NY-14216 >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > _______________________________________________ >> >> >>> >> > Freesurfer mailing list >> >> >>> >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >> >>> >> -- >> >> >>> >> Douglas N. Greve, Ph.D. >> >> >>> >> MGH-NMR Center >> >> >>> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> >> >>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> >> >>> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> >>> >> >> >> >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >>> >> Outgoing: >> >> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >>> >> >> >> >>> >> _______________________________________________ >> >> >>> >> Freesurfer mailing list >> >> >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >> >>> >> >> >> >>> >> The information in this e-mail is intended only for the person >> to >> >> >>> whom >> >> >>> >> it >> >> >>> >> is >> >> >>> >> addressed. If you believe this e-mail was sent to you in error >> >> and >> >> >>> the >> >> >>> >> e-mail >> >> >>> >> contains patient information, please contact the Partners >> >> Compliance >> >> >>> >> HelpLine at >> >> >>> >> http://www.partners.org/complianceline . If the e-mail was >> sent >> >> to >> >> >>> you >> >> >>> >> in >> >> >>> >> error >> >> >>> >> but does not contain patient information, please contact the >> >> sender >> >> >>> and >> >> >>> >> properly >> >> >>> >> dispose of the e-mail. >> >> >>> >> >> >> >>> >> >> >> >>> > _______________________________________________ >> >> >>> > Freesurfer mailing list >> >> >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >>> >> >> >>> -- >> >> >>> Shantanu Ghosh, Ph.D. >> >> >>> Harvard Medical School & Massachusetts General Hospital >> >> >>> Martinos Center for Biomedical Imaging >> >> >>> -- >> >> >>> Not only is the universe stranger than we think, it is stranger >> than >> >> we >> >> >>> can think. -Werner Heisenberg >> >> >>> >> >> >>> _______________________________________________ >> >> >>> Freesurfer mailing list >> >> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >> _______________________________________________ >> >> >> Freesurfer mailing list >> >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> > >> >> > -- >> >> > Shantanu Ghosh, Ph.D. >> >> > Harvard Medical School & Massachusetts General Hospital >> >> > Martinos Center for Biomedical Imaging >> >> > -- >> >> > Not only is the universe stranger than we think, it is stranger >> than >> >> we >> >> > can think. -Werner Heisenberg >> >> > >> >> > >> >> >> >> >> >> -- >> >> Shantanu Ghosh, Ph.D. >> >> Harvard Medical School & Massachusetts General Hospital >> >> Martinos Center for Biomedical Imaging >> >> -- >> >> Not only is the universe stranger than we think, it is stranger than >> we >> >> can think. -Werner Heisenberg >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger than we >> can think. -Werner Heisenberg >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello Freesurfer, Thanks for your suggestion on recon-all, its working, I used what Markus suggested earlier and later by Dough. However, since its only for the T1 image how do I process the rest of images which are T2, T2* and DTI images?
Thanks and best regards,
Sampada
On Mon, May 19, 2014 at 2:04 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Use something like
recon-all -s s600a1001 -i s600a1001.mgz -all
On 05/15/2014 02:55 PM, Dr Sampada Sinha wrote:
Hello Shantanu I tried to set up the Subject directory using this command and it says the following error:
Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a directory cp: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory cat: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 Actual FREESURFER_HOME /Applications/freesurfer /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh <shantanu@nmr.mgh.harvard.edu mailto:shantanu@nmr.mgh.harvard.edu> wrote:
You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the currentone
with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/ and then run recon-all S. On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote: > Hello freesurfer, thanks for your message. I am doing the recon-all for T1 > and T2* structural dataset now I have in all 8 files in the order of > (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject > and > we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am > running this command for recon-all '-all' process. My two files (T1 and > T2*) are in the Vaibhav2 folder. > My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and > subject id is s600a1001.mgz > > sampada$ export FREESURFER_HOME=/Applications/freesurfer > > dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2 > > dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' > > ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz > > > Even when I make the intermediate directory of mri/orig, its still not > recognising the command and shows an error. > > > Thanks and regards, > > > Sampada > > > > On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh > <shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu >> wrote: > >> You should try to run recon_all command with -all flag to run on the >> structural T1 dataset. After that you can use the tutorials from the >> freesurfer wiki to do a Feat analysis. >> >> For recon_all you need to specify only the subject and the script >> automatically does the rest. Segmentation and parcellation is >> automatized >> (see wiki) >> >> Hth, >> Shantanu >> >> >> On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote: >> > Hello Freesurfer, >> > >> > Thanks Shantanu I was able to convert the .nii to .mgz files . >> However, >> > about the recon-all command do I run it separately for each .mgz file >> or >> > run it one time for all .mgz file(which are eight in numbers)? And >> what >> > command do I use for recon-all? I have tried many but none is >> working.. >> > >> > Thanks and regards, >> > >> > Sampada >> > >> > >> > >> > >> > >> > >> > On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < >> > shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu>> wrote: >> > >> >> sorry >> >> >> >> try: >> >> >> >> cd Users/sampada/Desktop/ >> >> mkdir test >> >> cd test >> >> mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> >> sampada/Desktop/test/s400a1001.mgz >> >> >> >> Hth, >> >> shantanu >> >> >> >> On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: >> >> > You don't need the quotation marks in your path >> >> > also, it seems you don't have a directory called >> >> > /Users/sampada/Desktop/test/org >> >> > >> >> > try something like: >> >> > >> >> > cd Users/sampada/Desktop/ >> >> > mkdir test >> >> > cd test >> >> > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii >> >> > sampada/Desktop/test/s400a1001.nii >> >> > >> >> > Hth, >> >> > shantanu >> >> > >> >> > >> >> > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: >> >> >> Hello Shantanu, >> >> >> >> >> >> Many thanks for your reply! This is my exact commandline which I >> give >> >> to >> >> >> free surfer for the 1st of the eight nii files. When i am able to >> >> >> convert >> >> >> this nii to mgz then i will ask how to convert all the eight files >> at >> >> >> one >> >> >> go. >> >> >> >> >> >> mri_convert'/Users/sampada/Desktop/d2n119495/s400a1001.nii'
>> >> >> '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >> >> >> >> >> >> >> Regards, >> >> >> >> >> >> Sampada >> >> >> >> >> >> >> >> >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh >> >> >> <shantanu@nmr.mgh.harvard.edu <mailto:shantanu@nmr.mgh.harvard.edu> >> >> >>> wrote: >> >> >> >> >> >>> can you send your exact mri_convert commandline? >> >> >>> >> >> >>> >> >> >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: >> >> >>> > *Hello freesurfer* >> >> >>> > >> >> >>> > *Sorry for the personal message Shantanu. * >> >> >>> > >> >> >>> > *I managed to convert my dicom to nifti using mricron software, >> >> >>> though >> >> >>> had >> >> >>> > to make some changes to the preferences. * >> >> >>> > >> >> >>> > *About the dcmunpack: The user manual on dcmunpack on fs site >> says >> >> >>> that >> >> >>> > the >> >> >>> > unpackdcmdir is used only to unpack Siemens dicom files. We use >> >> >>> Phillips >> >> >>> > infinity for our PET scan.* >> >> >>> > >> >> >>> > *I am very new to Unix, free surfer and neuroimaging, so >> couldn't >> >> >>> > understand what nipy would do...* >> >> >>> > >> >> >>> > *My FS is working fine as when I typed tkmedit bert orig.mngz >> for >> >> >>> volume >> >> >>> > view it was displaying image.* >> >> >>> > >> >> >>> > *But the when I tried to convert my .nii files to .mgz format , >> I >> >> get >> >> >>> the >> >> >>> > following error:* >> >> >>> > >> >> >>> > >> >> >>> > Last login: Tue May 6 10:40:32 on ttys000 >> >> >>> > dhcp020-222-117:~ sampada$ export >> >> >>> FREESURFER_HOME=/Applications/freesurfer >> >> >>> > dhcp020-222-117:~ sampada$ source >> >> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >>> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >> >>> -------- >> >> >>> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >> >>> > FREESURFER_HOME /Applications/freesurfer >> >> >>> > FSFAST_HOME /Applications/freesurfer/fsfast >> >> >>> > FSF_OUTPUT_FORMAT nii.gz >> >> >>> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >> >>> > MNI_DIR /Applications/freesurfer/mni >> >> >>> > dhcp020-222-117:~ sampada$ mri_convert >> >> >>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' >> >> >>> > '/Users/sampada/Desktop/test/mri/org/.mgz' >> >> >>> > mri_convert/Users/sampada/Desktop/d2n119495/s400a1001.nii
>> >> >>> > /Users/sampada/Desktop/test/mri/org/.mgz >> >> >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp >> $ >> >> >>> > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... >> >> >>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 >> >> >>> > i_ras = (0.0268034, -0.99958, 0.0110098) >> >> >>> > j_ras = (0.0381548, 0.0120287, 0.999199) >> >> >>> > k_ras = (0.998912, 0.0263618, -0.0384612) >> >> >>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz... >> >> >>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could >> not >> >> >>> open >> >> >>> > file >> >> >>> > >> >> >>> > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz >> >> >>> > >> >> >>> > >> >> >>> > *Will you please let me know what command I need to use to mri >> >> >>> convert >> >> >>> and >> >> >>> > recon all of my files? * >> >> >>> > I* have 8 .nii files (in the order of >> T1>T2>T1>T2>DTI>T1(resting >> >> >>> stage)>T2 >> >> >>> > (in the order of the acquisition acquired at the time of >> >> >>> experiment).* >> >> >>> > >> >> >>> > >> >> >>> > *Thanks and regards,* >> >> >>> > >> >> >>> > *Sampada* >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve >> >> >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> >> >>> >> wrote: >> >> >>> > >> >> >>> >> >> >> >>> >> Have you tried using dcmunpack? You run it twice, once without >> >> any >> >> >>> >> output to get a list of runs in the folder. The 2nd with how >> you >> >> >>> want >> >> >>> >> the data converted. Run it with --help to get more info >> >> >>> >> doug >> >> >>> >> >> >> >>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> >> >>> >> > Hello I have only recently started the fmri data analysis >> and I >> >> >>> >> > downloaded freesurfer point by point from martinos site and >> >> >>> >> > incorporated the license file as well into the >> >> >>> Applications/freesurfer >> >> >>> >> > directory. I have run into the first problem and that is of >> >> data >> >> >>> >> > conversion. My file is in dcm format and I have 11,000 dcm >> >> files >> >> >>> to >> >> >>> >> > convert. However, before I was using Jamaan Alghamadi >> created >> >> gui >> >> >>> and >> >> >>> >> > it is not able to convert the mri dcm files. Then I shifted >> to >> >> >>> UNIX >> >> >>> >> > and again it is saying error. >> >> >>> >> > >> >> >>> >> > My file is on the desktop and I have given it subject id as >> >> Grace. >> >> >>> My >> >> >>> >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> >> >>> >> > >> >> >>> >> > My terminal look like this before I proceed with the file >> >> >>> conversion >> >> >>> >> > >> >> >>> >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> >> >>> >> > >> >> >>> >> > dhcp020-223-179:~ sampada$ export >> >> >>> >> FREESURFER_HOME=/Applications/freesurfer >> >> >>> >> > >> >> >>> >> > dhcp020-223-179:~ sampada$ source >> >> >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >>> >> > >> >> >>> >> > -------- >> freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >> >>> -------- >> >> >>> >> > >> >> >>> >> > Setting up environment for FreeSurfer/FS-FAST (andFSL)
>> >> >>> >> > >> >> >>> >> > FREESURFER_HOME /Applications/freesurfer >> >> >>> >> > >> >> >>> >> > FSFAST_HOME /Applications/freesurfer/fsfast >> >> >>> >> > >> >> >>> >> > FSF_OUTPUT_FORMAT nii.gz >> >> >>> >> > >> >> >>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> >> >>> >> > >> >> >>> >> > MNI_DIR /Applications/freesurfer/mni >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Will anyone please let me know what I am doing wrong? I will >> be >> >> >>> very >> >> >>> >> > grateful for any input. >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Thanks and regards, >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > Sampada >> >> >>> >> > Senior research support specialist >> >> >>> >> > Molecular and neuroimaging department >> >> >>> >> > Department of Psychiatry >> >> >>> >> > 451, biomedical research building >> >> >>> >> > University at Buffalo (south campus) >> >> >>> >> > Buffalo, NY-14216 >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > _______________________________________________ >> >> >>> >> > Freesurfer mailing list >> >> >>> >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >> >>> >> -- >> >> >>> >> Douglas N. Greve, Ph.D. >> >> >>> >> MGH-NMR Center >> >> >>> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> >> >>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> >> >>> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> >>> >> >> >> >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >>> >> Outgoing: >> >> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >>> >> >> >> >>> >> _______________________________________________ >> >> >>> >> Freesurfer mailing list >> >> >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >> >>> >> >> >> >>> >> The information in this e-mail is intended only for the person >> to >> >> >>> whom >> >> >>> >> it >> >> >>> >> is >> >> >>> >> addressed. If you believe this e-mail was sent to you in error >> >> and >> >> >>> the >> >> >>> >> e-mail >> >> >>> >> contains patient information, please contact thePartners
>> >> Compliance >> >> >>> >> HelpLine at >> >> >>> >> http://www.partners.org/complianceline . If the e-mail was >> sent >> >> to >> >> >>> you >> >> >>> >> in >> >> >>> >> error >> >> >>> >> but does not contain patient information, please contact the >> >> sender >> >> >>> and >> >> >>> >> properly >> >> >>> >> dispose of the e-mail. >> >> >>> >> >> >> >>> >> >> >> >>> > _______________________________________________ >> >> >>> > Freesurfer mailing list >> >> >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >> >> >>> >> >> >>> -- >> >> >>> Shantanu Ghosh, Ph.D. >> >> >>> Harvard Medical School & Massachusetts General Hospital >> >> >>> Martinos Center for Biomedical Imaging >> >> >>> -- >> >> >>> Not only is the universe stranger than we think, it is stranger >> than >> >> we >> >> >>> can think. -Werner Heisenberg >> >> >>> >> >> >>> _______________________________________________ >> >> >>> Freesurfer mailing list >> >> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >>> >> >> >> _______________________________________________ >> >> >> Freesurfer mailing list >> >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > >> >> > >> >> > -- >> >> > Shantanu Ghosh, Ph.D. >> >> > Harvard Medical School & Massachusetts General Hospital >> >> > Martinos Center for Biomedical Imaging >> >> > -- >> >> > Not only is the universe stranger than we think, it is stranger >> than >> >> we >> >> > can think. -Werner Heisenberg >> >> > >> >> > >> >> >> >> >> >> -- >> >> Shantanu Ghosh, Ph.D. >> >> Harvard Medical School & Massachusetts General Hospital >> >> Martinos Center for Biomedical Imaging >> >> -- >> >> Not only is the universe stranger than we think, it is stranger than >> we >> >> can think. -Werner Heisenberg >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger than we >> can think. -Werner Heisenberg >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Shantanu Ghosh