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