Freesurfer

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30132 discussions

mris_preproc --qdec-long problem
by Martin Reuter 07 Jun '13

07 Jun '13

Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: > Dr. Reuter, > > We corresponded in the past about QDEC, and you gave me great help. > The lab I work for is now moving towards using the Longitudinal Mixed > Effects Model. When I go to run the command: > > mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target > study_average --hemi lh --meas thickness --out lh.thickness.mgh > > I get the error: 'ERROR: no subjects specified.' I am attaching my > long.qdec.table.dat, which works fine when loaded by QDEC. Do you > have any idea of why I am getting this error? > > Thanks, > > Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Control points: possible bug (only tested in 5.3)
by Garikoitz Lerma-Usabiaga 07 Jun '13

07 Jun '13

Hi list, I've been creating control points and I got the following error: MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat): could not open file No such file or directory I created the /tmp/ folder by hand and then it created the control.dat file properly (going to tkmedit > File > Save Control Points). These are the permission on the S_11 folder: drwxrwxr-x 17 glerma domain users 4096 Jun 7 09:41 S_11 (this is a CentOS 5 machine) thanks! Gari

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R: Re: R: R: Re: R: Re: Tracula
by stdp82＠virgilio.it 06 Jun '13

06 Jun '13

The file that I have downloaded is named "unKnow" and it is of 7.6 MB. I have placed it in $FREESURFER_HOME/bin directory but the error persist. Anastasia, I apologize. Please, have patience with me :-) but .. when I search for "mris_resample" in mail list I did not found any indication. I found my previous mail and first Zeke response. Thanks, Stefano ----Messaggio originale---- Da: lzollei(a)nmr.mgh.harvard.edu Data: 6-giu-2013 23.20 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: R: Re: Tracula HI, A patch is now available for the "mris_resample : Command not found" error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample --Lilla On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I have resolved the previous problem by writing configuration file with sudo nano in command line. > > Now I'm running trac-all -prep but I have this error: > > > writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > > What's happened? > > Thanks, > > > Stefano > > > > ----Messaggio originale---- > Da: stdp82(a)virgilio.it > Data: 6-giu-2013 0.51 > A: <ayendiki(a)nmr.mgh.harvard.edu> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: [Freesurfer] R: Re: R: Re: Tracula > > I obtain /Applications/freesurfer/subjects/subject_prova > my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 6-giu-2013 0.42 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: Tracula > > > What do you get when you run "echo $SUBJECTS_DIR"? > > On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > > configuration file start normally and this no. > > Do you note some line that might be wrong additionally to setenv > > SUBJECTS_DIR line. > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-giu-2013 16.09 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: Tracula > > > > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > > SUBJECTS_DIR, see the example configuration file on the wiki and under > > $FREESURFER_HOME/bin/dmrirc.example. > > > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list and Anastasia, > > > I'm performing a set of data with tracula version 3.0. I have change my > > > dmrirc file respect to previous analyses and now I have one problem > > > > > > "set: Variable name must begin with a letter. > > > ERROR: must specify as many DWI dicoms as subjects". > > > > > > I do not find the line that is wrong. I think to have approximately used > > the > > > same lines of previous and correct analysis. > > > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > > > Thanks and best regards. > > > > > > > > > Stefano > > > > > > > > > > > > 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(a)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(a)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.

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field of value too small, wrap-around
by Maria Kharitonova 06 Jun '13

06 Jun '13

Hello, We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions? I'm pretty new to FreeSurfer, so I apologize in advance if this questions is naive. Thanks! Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital

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R: R: Re: R: Re: Tracula
by stdp82＠virgilio.it 06 Jun '13

06 Jun '13

Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in command line. Now I'm running trac-all -prep but I have this error: writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found. What's happened? Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 6-giu-2013 0.51 A: <ayendiki(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Tracula I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Tracula What do you get when you run "echo $SUBJECTS_DIR"? On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > configuration file start normally and this no. > Do you note some line that might be wrong additionally to setenv > SUBJECTS_DIR line. > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-giu-2013 16.09 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: Tracula > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > SUBJECTS_DIR, see the example configuration file on the wiki and under > $FREESURFER_HOME/bin/dmrirc.example. > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi list and Anastasia, > > I'm performing a set of data with tracula version 3.0. I have change my > > dmrirc file respect to previous analyses and now I have one problem > > > > "set: Variable name must begin with a letter. > > ERROR: must specify as many DWI dicoms as subjects". > > > > I do not find the line that is wrong. I think to have approximately used > the > > same lines of previous and correct analysis. > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > Thanks and best regards. > > > > > > Stefano > > > > > > > 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(a)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.

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Re: [Freesurfer] Still confused by group analysis..
by Tudor Popescu 06 Jun '13

06 Jun '13

Thanks Doug, > So if I want to use the study-specific "average" subject surface with >> mri_surf2surf, rather than the generic "fsaverage" one, how can this be >> done given that the required ls.white file only exists in the latter but >> not in the former? Can I just rename (or duplicate) ls.white into >> ls.white_avg? >> >> You can copy it or create a symbolic link. So it is OK to copy the required lh.white file from the generic average subject "fsaverage" and apply mri_surf2surf upon the study-specific average subject ("average")? It still seems to me that "average" should have its own (different) lh.white... > >> Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the >> group tutorial, the former is "lh.gender_age.thickness.10.**mgh" while >> the latter is "lh.gender_age.thickness.10B.**mgh". Or should it just be >> the unsmoothed output of mris_preproc? >> >> Yes, I can't remember why I put the "B" there, maybe to keep people from > overwriting lh.gender_age.thickness.10.mgh during the tutorial and having > to wait the 10min or so for it to get recreated. But if all these commands transform the same file (output of mris_preproc becomes input of mri_surf2surf, which then feeds into mri_glmfit), then why is it still necessary to keep intact the original lh.gender_age.thickness.10.mgh, when all you need for the group analysis is the mri_surf2surf'd version? > >> Assuming the label files (corresponding to my ROI, and extracted from the >> Destrieux atlas) are different for each subject, and given mri_glmfit is >> called just once, for all subjects, which label file (corresponding to what >> subject) should I point it to? >> >> You need to create the label in the average subject. There is a > Destrieux atlas there. Again, by "average subject" do you mean here the generic one (fsaverage) or the study-specific one (average)? Should the former be used at any point of a group analysis, if the latter exists?

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Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 17
by McMains, Stephanie 06 Jun '13

06 Jun '13

Here is the original thread (to at least most of it). Maybe I am just an idiot, but I cant' figure out how to easily reply from the web to an entire thread, and pulling it out of the digests I get is a pain!! They wanted to take an ROI from SPM and put it into free surfer to extract cortical thickness. I thought going through fsaverage was a good way to do this. But as I said, looking at the surface, I have some concerns. I am more confused by when you tell them to run the MNI template through recon-all to get a surface, because I thought fsaverage was a kind of MNI space that has already been run through? Thanks, Stephanie what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you for your response! I am still a bit confused about the vol2surf > command. I have a volumetric mask with voxels of interest based on a VBM > analysis in SPM. I would like to extract the cortical thickness measurements > based on these voxels. I am not clear what specifications I need to include > when using vol2surf. For example, what do I use as my registration matrix? > > Thank you for your help! > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > > > -----Original Message----- > From: freesurfer-boun...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, June 04, 2013 1:48 PM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness > > > Make sure that your SPM volume is registered to the anatomical, then use > mri_vol2surf to map the volume to the surface, then mri_segstats to extract > the mean of the thickness > > doug > > > > > On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: >> main lab: (617) 355-0400 > Dear FreeSurfer Experts, > > I was wondering if anyone can advise on the best way to use an ROI mask > created in SPM (XjView) to extract cortical thickness values in freesurfer. > > Thank you in advance for your help! > > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > <mailto:olga.ozra...@childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > Then it goes on: Hi Ola, this probably will not work. The tal coordinate is notoriously inaccurate in cortex. You are verylikely to totally miss the area you are looking for. A better way is to run the MNI template through recon-all, map your VBM result to the surface of that, then use mri_surf2surf to map the effect to each individual. doug On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you, again! I decided to try to use the Talairach coordinates from my > analysis for ROI extraction. I created an average subject and preprocessed > the data (mris_preproc). I obtained the vertex index based on the coordinates > from the average subject. Any ideas on how I can now find the corresponding > vertices in all my subjects? > > Thanks very much! > Ola > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422

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The feasibility of this procedure
by 淼 06 Jun '13

06 Jun '13

Dear FS, I want to do an analysis with freesurfer but this is relatively complicated. I would like to know whether this is doable by freesurfer. I first want to create a custom template based on my subjects and I have seen the SurfaceRegAndTemplate page and this should be the place where I should start. Then I should use mris_register to register all my subjects to the new template. Then I want to export volume data of each region of interest and total intracranial volume of subjects to SPSS for further analysis and I don't have a clue on how to do that yet. Do you think this is feasible? Any problems there? Thanks for any help in advance. Miao Sent from my iPhone

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averaging tracts?
by Hoptman, Matthew 06 Jun '13

06 Jun '13

Hi all, Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Enquire about running FreeSurfer {Disarmed}
by pablo najt 06 Jun '13

06 Jun '13

Hello I have a question regarding the installation/running FreeSurfer.I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot.However when I follow the steps for testing (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer) I always get "command not found". I was wondering if you would be able to help me.Thanks,Pablo

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