Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

strange freeview issue
by Satrajit Ghosh 03 Oct '11

03 Oct '11

hi, we are seeing a strange freeview issue at mit and just wanted to check if anybody else has seen this. we are running natty narwhal (ubuntu 11.04). details here: https://github.com/gablab/mindhive/issues/1 cheers, satra

3 5

tracula bvecs bvals error
by Joana Braga Pereira 01 Oct '11

01 Oct '11

Dear Freesurfers, I'm pre-processing my DTI data with Tracula and i found the following error while running trac-all -prep -c dmrirc_H_P01: dtifit -k /home/joana/FIU/H_P01/dmri/dwi.nii.gz -m /home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /home/joana/FIU/H_P01/dmri/bvecs -b /home/joana/FIU/H_P01/dmri/bvals -o /home/joana/FIU/H_P01/dmri/dtifit *Error: bvecs and bvals don't have the same number of entries* Linux ub029113 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS Although i saw a previous email reporting the same problem i wasn't able to solve it following that email's instructions... I think there is something wrong with my bvec file since dmri/bvecs.txt only contains zeros. I've tried changing bvec.txt columns to three decimals and then to 1, -1 and 0 but nothing seems to work. I've attached my bvals and bvecs files. Does anyone have any idea why this is happening? Many thanks to you all! Joana

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structure volume dti_recon vs recon_all
by Adil Javed 01 Oct '11

01 Oct '11

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of various structures for the same brain. Just trying to understand why that is? best, AJ

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Default for fwhm while running mri_glmfit
by Antonella Kis 30 Sep '11

30 Sep '11

----- Forwarded Message ----- From: Antonella Kis <atorok9(a)yahoo.com> To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Sent: Friday, September 30, 2011 12:31 PM Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit I see.I am not sure what exactly you mean by an outlier in my data,but if there will be an outlier, why the mri_glmfit --sim is working for a smoothing level 15? Also what means in your last sentence "when the smoothing level is only 20"? Isn't 20 the max smoothing level? And while smoothing level increases shouldn't fwhm increase? How different will be my results from the real one if I change the fwhm value from 31.843147 in the mri_glmfit.log file to a value of 30 and the run mri_glmfit-sim? I tried this and I am not getting the error any more but there are more clusters coming up and I have a different size for original clusters so I suppose the cortical thickness values cached in the tables are not good. Can I do this trick? Many thanks, AK ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Friday, September 30, 2011 11:40 AM Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit There is no one smoothing level that is right. In general, people tend to just go with a default value. I think that 20 is pretty high, I usually go with 5-15. You might examine your data to see if you have an outlier. I think it is unusual for you to get an output fwhm of over 30 when the smoothing level is only 20. doug Antonella Kis wrote: > > > Hi Doug, > > > Thanks for helping again. I used smoothing level of 20 because I was > told to use this smoothing. If I use the 15 I am not getting the > error but I need to use the 20.Is there a way that I can make it > work/correct this error and get my tables cached in this case? > > Is fwhm= 15 the default in FS while running the mri_gmlfit > (mri_surfcluster? What if my data was smoothed at 10 while running the > mris_preproc --cache-in thickness.fwhm20.fsaverage \ > > > Please advise. > Thank you. > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" > <freesurfer(a)nmr.mgh.harvard.edu>; "fischl(a)nmr.mgh.harvard.edu" > <fischl(a)nmr.mgh.harvard.edu> > *Sent:* Friday, September 30, 2011 10:52 AM > *Subject:* Re: Error due to fwhm > > That exceeds the valued for which the tables are cached. What > smoothing level did you use? > doug > > Antonella Kis wrote: > > > > Hi, > > > > When I ran the QDEC on patients with abnormal side right, the fwhm > for the clusters at thresh 2 is fwhm = 31.843147. > > Then, I ran mri_glmfit-sim on the QDEC output and it gives me the > following error (cannot find fwhm 32): > > > > ERROR: cannot find > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd > > > > Is there a way that I can change the fhwm while running > mri_glmfit-sim from 32 to 31.843147 or how I can correct this error? > > > > > > Many thanks. > > AK > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > Hi Doug, > > > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extracting longitudinal rate stats using cluster annot files
by Robustelli, Briana (NIH/NIMH) [F] 30 Sep '11

30 Sep '11

Hello Freesurfer team, I have been running a longitudinal analysis and have just finished analyzing the data in qdec and running a cluster correction. I would now like to use the significant cluster annot files to extract the thickness rate stats for each subject and put them in a table. I am a little confused how to do this with a longitudinal dataset. It seems I am unable to use annotation2label with fsaverage to change the annot file to label files. What brain is qdec using to display the longitudinal results? Is it fsaverage as usual or a different average brain? From there I am not sure which directories to use to extract rate stats. Are they kept in the base directories or each time point (XX1, XX2, or XX1.long.XX_base)? I would really appreciate a step by step guide of which programs to use and on what files, to be able to extract stats for each subject using significant clusters as ROIs. I hope my question is clear and thank you for your time. Best, Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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Hippocampal Subfield Masks
by Shashwath Meda 30 Sep '11

30 Sep '11

Hi all - What would be the best way to create ROI masks of the individual hippo subfields that are generated in Freesurfer? Thanks! Shashwath Meda

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Re: [Freesurfer] Error due to fwhm
by Antonella Kis 30 Sep '11

30 Sep '11

Hi Doug, Thanks for helping me again. I used smoothing level of 20 because I was told to use this smoothing. If I use the 15 I am not getting the error but I need to use the 20.Is there a way that I can make it work/correct this error and get my tables cached in this case? Please advise. Thank you. AK ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>; "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu> Sent: Friday, September 30, 2011 10:52 AM Subject: Re: Error due to fwhm That exceeds the valued for which the tables are cached. What smoothing level did you use? doug Antonella Kis wrote: > > Hi, > > When I ran the QDEC on patients with abnormal side right, the fwhm for the clusters at thresh 2 is fwhm = 31.843147. > Then, I ran mri_glmfit-sim on the QDEC output and it gives me the following error (cannot find fwhm 32): > > ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd > > Is there a way that I can change the fhwm while running mri_glmfit-sim from 32 to 31.843147 or how I can correct this error? > > > Many thanks. > AK > > -- 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 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. Hi Doug,

2 2

hippocampus segmentation
by George Kanw 30 Sep '11

30 Sep '11

Sorry to ask a trival question: After hippocampus segmentation, how can I extract the coordinates of each subregion? The general matlab functions seem unable to read the info. Thanks in advance, George

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Error due to fwhm (ASAP please)
by Antonella Kis 30 Sep '11

30 Sep '11

Hi Doug, I believe I got the error for the Abnormal Side R because the fwhm for the clusters with thresh 2 in QDEC is fwhm = 31.843147 as you can see below: and when I run mri_glmfit-sim it gives me the error: and when I run mri_glmfit-sim it gives me the error that cannot find fwhm 32: ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd Is three a way that I can change the fhwm while running mri_glmfit-sim from 32 to 31.843147 or how I can correct this error? MAny thanks. AK

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Tool for filling
by Ed Gronenschild 30 Sep '11

30 Sep '11

Hi, I'm looking for a tool to fill holes of only 1 voxel in size in a binary mask. I posted this also to the FSL mailing list but none of the suggested solutions could do this or were robust enough. Ed

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Freesurfer September 2011