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
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