Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Regarding cortical thickness
by Bharti Rana 14 Apr '13

14 Apr '13

I am Bharti, a M.Tech./Ph.D student at School of Computer & Systems Sciences, Jawaharlal Nehru University, New Delhi, India. My area of interest is pattern recognition and image processing. In one of my research work, i used freely available freesurfer software to find cortical thickness using recon-all -all command. But, while retrieving cortcal thickness maps using read_curv() function, i am getting different number of vertices for different brains. Are different number of cortical vertices possible for two different brains? I have gone through FAQ provided by Freesurfer but i did not find any related answer. Kindly clarify. Thanks in advance. -- Best Regards Bharti M.Tech./Ph.D. School of Computer & Systems Sciences Jawaharlal Nehru University NEW DELHI, INDIA

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Re: [Freesurfer] Error from mri_concat while using QDEC
by Tudor Popescu 03 Apr '13

03 Apr '13

Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file? Anyway, after trying out the command with only one of the files from the tutorial, *mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh* ..the same thing happens, namely it returns to the command prompt, with no message whatsoever. What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help! Tudor On 20 December 2012 05:24, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > That does not make sense. Try using only one input file. Also, put --debug > as the first option. > doug > > > > > > > On 12/19/12 8:32 AM, Tudor Popescu wrote: > > Hi Doug, > So the full command is > > mri_concat > /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh > --o > /media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh > --debug > > ..however, as soon as I press Enter, I'm just taken to the command prompt > again, with no output whatsoever! Am I calling mri_concat wrongly?! > > Tudor > > On 18 December 2012 17:15, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> Hi Tudor, >> Can you run mri_concat from the command line with the --debug option >> first. Send us the FULL command line and the full terminal output. >> doug >> >> >> >> On 12/18/2012 09:35 AM, Tudor Popescu wrote: >> > Hello everyone, >> > >> > I tried doing the QDEC group analysis tutorial, however after doing >> > everything as instructed in the tutorial, when pressing Analyze I get >> > the error message: >> > >> > /Error in Analyze: command failed: mri_concat >> > >> /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh >> > >> /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh >> > (..)/ >> > >> > ..even though those files are all accessible there! I pasted that same >> > mri_concat manually into the terminal, however no output is produced >> > at the command prompt, nor any files are created. >> > >> > In previous attempts, I used to also get this error >> > >> > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in >> > SUBJECTS_DIR "/ >> > /Syntax error: Bad fd number"/ >> > >> > after following the sh/bash workaround from this >> > < >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h… >> >previous >> > thread, I no longer get that error, however get stuck with the error >> > mentioned above. >> > >> > My SUBJECTS_DIR already contains a copy of the default subjects folder. >> > >> > Debug info below. Any help greatly appreciated! >> > Tudor >> > >> > -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > FREESURFER_HOME /home/virtualuser/freesurfer >> > FSFAST_HOME /home/virtualuser/freesurfer/fsfast >> > FSF_OUTPUT_FORMAT nii.gz >> > SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects >> > MNI_DIR /home/virtualuser/freesurfer/mni >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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] Error with .license after upgrading to 5.2
by Nicola Toschi 02 Apr '13

02 Apr '13

Hi - no luck unfortunately (I had already tried changing permissions).... On 03/22/2013 04:09 PM, Varghese Chikku wrote: > Hi Nicola, > Can you try this command,and echo the license.It may ask for > password.I have similar issues with 5.2 and this how i sorted. > sudo chmod -R a+rwX /Applications/freesurfer > then > echo each line of the licence. > Let me know > In thanks > chikku

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How to get surface-based AAL template
by ZhiLiangLong 01 Apr '13

01 Apr '13

Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes.

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Problem with longitudinal edits
by Vy Dinh 01 Apr '13

01 Apr '13

Dear Developers, I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized. We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem: recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) *Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? * * * *What solutions would you suggest in resolving this problem?* * * Thank you, Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center

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More QDEC questions
by Tudor Popescu 01 Apr '13

01 Apr '13

Hi everyone, My QDEC analysis ran into an error message that seems to be a "classic" (and, so far, it seems unsolved), from mri_concat, which I've described in a separate message, just sent. I have, however, more theoretical questions about QDEC, which I hope some kind soul will help me with: - why does QDEC only provide the volume of *subcortical* structures under StatsDataImport/aseg.volume, when the automatic GM/WM segmentation is done for the entire brain, not just for subcortical regions? - how are the volume measurements provided in aseg.volume different from the ones done obtained with a VBM analysis? - why is *volume *the result of *segmentation *(aseg.volume) whereas *thickness *derives from *parcelation *(rh.aparc.thickness)? Is it not the case that both operations (segmentation+parcellation) are necessary to calculate volume as well as thickness? - how is a QDEC thickness analysis different from a regular AN(C)OVA in which you are interested in main and interaction effects of the IVs on the DV? I ask this because some of the questions that appear in QDEC's Analysis Results tab – e.g. "is the correlation between (DV) and (IV) different from zero?" – would not (I think) be directly answerable by an ANOVA - would the same type of ANOVA done by QDEC be doable by extracting the values of the DV for each subject (using e.g. *aseg.volume*) and then doing the ANOVA in e.g. SPSS? If so, when would you do one versus the other? - why is it that only continuous factors (e.g. age) can be taken in the analysis as nuisance factors, when discrete variables (e.g. gender) might also be irrelevant for a particular analysis and thus belong to the Nuisance Factor list? Many thanks in advance!! Tudor

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FS 5.2 asegstats2table is not found or is too small to be a valid stats file error
by Salil Soman 31 Mar '13

31 Mar '13

Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files * Any suggestions on what I am doing incorrectly? I would like to extract all of the statistics in aseg.stats into a single row per subject to facilitate additional analysis in other programs. Any suggestions on how to accomplish this would be much appreciated. Thank you. -S* *

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mri_glmfit-sim doesn't recognize --label flag
by Yizhou Ma 31 Mar '13

31 Mar '13

Dear freesurfer experts, I'm doing small volume correction for multiple comparison. However, when I run "mri_glmfit-sim" with "--label mylabelfile", I got the error that "--label unrecognizable". I use "mri_glmfit-sim --help" to see the help information but there is no information regarding "--label" or "--mask". May I know why this? P.S. I use FS510. I have run mri_glmfit-sim successfully without a mask. Thanks, Cherry

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tractstats@table output oddity
by Jon Wieser 31 Mar '13

31 Mar '13

I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list "fmajor_file_list.txt" it produced the output file "fmajor_table.txt" (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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denominator of the t-test in fsfast?
by Alex Kell 31 Mar '13

31 Mar '13

freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual * c*(X' * X)^-1*c' where X is the stim matrix and c is the contrast vector and ' denotes transpose two questions: 1. i tried computing cesvar myself, but it is not the equation above (for the one subject i was playing with, cesvar was ~1.5x the above equation). what is the equation that is used? 2. intuitively, the second half of that [ c*(X' * X)^-1*c ] penalizes for correlations in your stimulus matrix, particularly for those relevant to your contrast. is that a good way to think about it? thanks in advance! alex

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Freesurfer March 2013