[Freesurfer] inqiury
Dear FS developers, I wish to transform DICOM format to omgz format. However, we have problem when we tried to do recon-all command. The error is as follow: bash-3.2$ export FREESURFER_HOME=/applications/freesurfer bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni bash-3.2$ sudo recon-all -s 'aaa' -i /Users/Dannydeng/desktop/danny_mri/MR22022/DICOM/IM_0001 Password: FREESURFER_HOME: Undefined variable. bash-3.2$ Thanks. Best Regards, Danny Deng ___ 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.
Re: [Freesurfer] Recon-all -hires
Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified) Xues-MacBook-Air:0001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:0001 DannyDeng$ Please help. Thanks. Best Regards, Danny Deng > On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee <hweeling@gmail.com> wrote: > > Dear Bruce, > > Thanks for your reply. > I checked the folder and did not find the file that was requested. > > What I have in the average folder that has 'RB*.gca' are > 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. > The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. > > Cheers, > Hweeling > > On Nov 21, 2017 18:05, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > Hi Hweeling > > what is FREESURFER_HOME set to in the environment? Does that file exist? It > is a standard part of our distribution > > cheers > Bruce > > > On Tue, 21 Nov 2017, Hwee Ling Lee wrote: > > Dear all, > > I have T1 images collected from the 7T MRI scanner. > > I downloaded the most recent freesurfer software, and followed all > instructions to install the software before using it. > > I would like to segment the T1 data using its high resolution image, and > also to segment the hippocampal subfields. > > For command, I use this: > > recon-all -all -s -hires -i location> > > However, I get an error message: > > cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca > > I'm not sure what I did wrong. > > Also, how can I combine high resolution segmentation and hippocampal > subfields segmentation? > > Could someone please help? > > Thanks. > > Best regards, > Hweeling > > > > > > 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 > <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 > > > 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 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.
Re: [Freesurfer] problems of testing freesurfer
Hi Andrew,
I have followed your suggestion and the error pop up like this:
Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects
mkdir: test_subjects: File exists
Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects/sample-001.nii.gz
-bash: cd/Applications/freesurfer/subjects/sample-001.nii.gz: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects
-bash: cd/Applications/freesurfer/subjects: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd ${FREESURFER_HOME}/subjects
Xues-MacBook-Air:subjects DannyDeng$ recon-all -i sample-001.nii.gz -s bert -all
ERROR: cannot find sample-001.nii.gz
Darwin Xues-MacBook-Air.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Nov 8 16:50:37 HKT 2017
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Xues-MacBook-Air:subjects DannyDeng$
Sorry I am a beginner.
Best Regards,
Danny Deng
> On Nov 8, 2017, at 10:48 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote:
>
> recon-all -i sample-001.nii.gz -s bert -all
>
___
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] problems of testing freesurfer
Hi developers, I just installed the software and there are so many problems I wish to seek help from you when I tried “Test your freesurfer installation” on the website Example 2 I tried several commands as follow but all failed: 1. Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=<$FREESURFER_HOME/subjects/sample-001.mgz .> -bash: syntax error near unexpected token `newline’ 2. Xues-MacBook-Air:~ DannyDeng$ > export SUBJECTS_DIR= -bash: syntax error near unexpected token `newline’ 3. Xues-MacBook-Air:~ DannyDeng$ >export SUBJECTS_DIR=<_HOME/subjects/sample-001.mgz .> -bash: syntax error near unexpected token `newline’ 4. DannyDeng$ DannyDeng$SUBJECTS_DIR -bash: DannyDengcp/Applications/freesurfer/subjects/sample-001.mgz: No such file or directory Besides, I think I can’t find nifti file in my freesurfer folder. example 3 Same problem like example 2: Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR= -bash: syntax error near unexpected token `newline’ example 4: Only this one I successfully opened it. Thanks very much. Best Regards, Danny Deng ___ 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.
Re: [Freesurfer] hemisphere analysis
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility is fine with my download version (MacOS Lion
OS X 10.7 (64b intel)Stable v6.0.0)
Please kindly suggest.
Thanks ver much
Best Regards,
Danny Deng
> On Nov 7, 2017, at 7:14 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
>
>
>
> On 11/06/2017 12:03 PM, lanbo Wang wrote:
>> Dear experts,
>>
>> I have two questions about hemisphere analysis:
>>
>> 1) When I run left-right hemisphere paired t-test, can I add age as
>> covariate? If use fsgd to add covariate, to this paired t-test
>> analysis, how to make the fsgd table?
> use this one-group, one-covariate example
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
>> 2) I want to reorganize the hemisphere from left-right to
>> symptom-nosymptom according to body symptom side record and compare
>> different between symptom hemisphere and nosymptom hemisphere. Can I
>> use freesurfer to do it?
> Yes, though it is a little tricky with multiple ways, each complicated
> in its own way.
> 1. Create your own design matrix. You can use the one created by
> mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then,
> in each subject whose symptomHemi is rh, multiply its line in the design
> matrix by -1. Then pass this design matrix to mri_glmfit with --X
> instead of passing an FSGD file.
> 2. Load the output of mris_preproc into matlab, eg, y =
> MRIread('y.mgh');, then change the sign as in #1 above, eg,
> y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable
> subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run
> mri_glmfit as normal with the new file.
> 3. Run mris_preproc for each subject separately to generate an
> lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in
> #1 above with
> fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o
> lh.lh-rh.thickness.sm00.subject10.mgh
> Then run mri_concat to concatenate all the subjects together in the same
> order as they are listed in the FSGD file, then use this stack as input
> the mri_glmfit
>
>>
>> Thanks for your patient and help.
>>
>> All best,
>> Lanbo Wang
>>
>>
>> ___
>> 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
> gr...@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
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] License issue
Dear FDs, According to the instructions, I have cut the 4 lines between the “CUT HERE”, copy and past the 4 lines into my license.txt file in the home directory to freesurfer folder as follow: --- PART C. MISCELLANEOUS This Agreement shall be governed by and construed in accordance with the laws of The Commonwealth of Massachusetts without regard to principles of conflicts of law. This Agreement shall supercede and replace any license terms that you may have agreed to previously with respect to FreeSurfer. dannytang...@gmail.com 33367 *CL6BxmQcdv6k FScW2..sWlD9c However,when I tried to test my installation using the sample-001, it shows the error message as follow: Xues-MacBook-Air:~ DannyDeng$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Xues-MacBook-Air:~ DannyDeng$ mri_Convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Xues-MacBook-Air:~ DannyDeng$ Please help. thanks However Best Regards, Danny Deng ___ 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] bug report 2
Dear Freesurfer developers, when I tried to perform example 3: perform a full recon-all on a preexisting subject folder The error occurs as follow: syntax error near unexpected token `newline’ I don’t know how to proceed further. please help. Thanks. Best Regards, Danny Deng > Begin forwarded message: > > From: Danny Deng <dannytang...@gmail.com> > Subject: Fwd: bug report > Date: November 5, 2017 at 9:08:54 PM GMT+8 > To: freesurfer@nmr.mgh.harvard.edu > >> Dear Freesurfer developers, >> >> I encountered a problem when I tried to open the sample-001. with >> information as follow: >> >> ERROR: Invalid FreeSurfer license key found in license file >> /Applications/freesurfer/license.txt >> If you are outside the NMR-Martinos Center, >> go to http://surfer.nmr.mgh.harvard.edu/registration.html >> <http://surfer.nmr.mgh.harvard.edu/registration.html> to >> get a valid license file (it's free). >> If you are inside the NMR-Martinos Center, >> make sure to source the standard environment. >> >> In fact I have already saved the license and directed from the desktop into >> my home directory. >> >> Please help. thanks so much! >> >> >> Best Regards, >> Danny Deng > > Best Regards, > Danny Deng > >> Begin forwarded message: >> >> From: Danny Deng <dannytang...@gmail.com <mailto:dannytang...@gmail.com>> >> Subject: bug report >> Date: November 5, 2017 at 9:04:43 PM GMT+8 >> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> >> Dear Freesurfer developers, >> >> I encountered a problem when I tried to open the sample-001. with >> information as follow: >> >> ERROR: Invalid FreeSurfer license key found in license file >> /Applications/freesurfer/license.txt >> If you are outside the NMR-Martinos Center, >> go to http://surfer.nmr.mgh.harvard.edu/registration.html >> <http://surfer.nmr.mgh.harvard.edu/registration.html> to >> get a valid license file (it's free). >> If you are inside the NMR-Martinos Center, >> make sure to source the standard environment. >> >> In fact I have already saved the license and directed from the desktop into >> my home directory. >> >> Please help. thanks so much! >> >> >> Best Regards, >> Danny Deng >> > ___ 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] Fwd: bug report
> Dear Freesurfer developers, > > I encountered a problem when I tried to open the sample-001. with information > as follow: > > ERROR: Invalid FreeSurfer license key found in license file > /Applications/freesurfer/license.txt > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu/registration.html > <http://surfer.nmr.mgh.harvard.edu/registration.html> to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > > In fact I have already saved the license and directed from the desktop into > my home directory. > > Please help. thanks so much! > > > Best Regards, > Danny Deng Best Regards, Danny Deng > Begin forwarded message: > > From: Danny Deng <dannytang...@gmail.com> > Subject: bug report > Date: November 5, 2017 at 9:04:43 PM GMT+8 > To: freesurfer@nmr.mgh.harvard.edu > > Dear Freesurfer developers, > > I encountered a problem when I tried to open the sample-001. with information > as follow: > > ERROR: Invalid FreeSurfer license key found in license file > /Applications/freesurfer/license.txt > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu/registration.html > <http://surfer.nmr.mgh.harvard.edu/registration.html> to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > > In fact I have already saved the license and directed from the desktop into > my home directory. > > Please help. thanks so much! > > > Best Regards, > Danny Deng > ___ 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.
