Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

Selxavg3-sess Out of Memory - What are the options?
by SHAHIN NASR 13 Jan '12

13 Jan '12

Hi, I am running selxavg3-sess under freesurfer 4.5 and I faced "out of memory error" as it started "computing whitening matrices". Since they are monkey datasets, runs were relatively long (12 runs each 16 min; TR=1.4). I want to know what options do I have here? Please note that, when I applied this command to 3 runs rather than all 12 runs (by making a runlist), I didn't face this error. P.S.: I can not use version 5.1 because we don't have structural scan for this monkey and we just want to check the functional scans without any registration. I assume it is not possible in version 5. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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selxavg3-sess issue in FSFAST
by Ivan Alvarez 13 Jan '12

13 Jan '12

Dear Freesurfers, I recently attempted my first FSFAST analysis following the tutorial on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt <http://nmr.mgh.harvard.edu/%7Egreve/fsfast.intro.ppt> while using my own data. I stumbled across an error in selxavg3-sess which I can't decipher. The problem seems to arise when running the Matlab script fast_selxavg3.m andra returns: outtop = /media/data/analysis/FREESURFER_TEST/Project Extension format = nii.gz Error using basename Too many input arguments. Error in fast_ldanaflac (line 423) nuisregevname = basename(nuisreg,'dat'); % remove .dat Error in fast_selxavg3 (line 53) flac0 = fast_ldanaflac(analysis); I have looked through the Freesurfer documentation and mailing list but couldn't spot anyone with this issue. I am attaching the full log below, any insights would be greatly appreciated! ivan@sirsa:/media/data/analysis/FREESURFER_TEST/Project$ selxavg3-sess -sf sessid -analysis verbgen.sm5.lh Surface data fsaverage lh -------------------------------------------------------------- selxavg3-sess logfile is /media/data/analysis/FREESURFER_TEST/Project/log/selxavg3-sess-bold-verbgen.sm5.lh-120112125113.log -------------------------------------------------------------- preproc-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ ivan setenv FREESURFER_HOME /home/ivan/freesurfer setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC 2011 x86_64 GNU/Linux /media/data/analysis/FREESURFER_TEST/Project /home/ivan/freesurfer/fsfast/bin/preproc-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog Thu Jan 12 12:51:13 GMT 2012 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain Sess01 Template ----------------------------- mktemplate-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -nolog -update Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 ---------------- Thu Jan 12 12:51:13 GMT 2012 Detected input format at nii Sess01 Update not needed Run: 001 ---------------- Thu Jan 12 12:51:13 GMT 2012 Sess01 001 Update not needed Run: 002 ---------------- Thu Jan 12 12:51:13 GMT 2012 Sess01 002 Update not needed Thu Jan 12 12:51:13 GMT 2012 mktemplate-sess completed Sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -nolog -update ------------------------------------------------ /media/data/analysis/FREESURFER_TEST/Project/Sess01 Thu Jan 12 12:51:13 GMT 2012 Sess01 Update not needed for session-level mask Sess01 Update not needed for run 001 mask Sess01 Update not needed for run 001 meanval Sess01 Update not needed for run 002 mask Sess01 Update not needed for run 002 meanval Thu Jan 12 12:51:13 GMT 2012 mkbrainmask-sess done Sess01 Registration ----------------------------- register-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Thu Jan 12 12:51:13 GMT 2012 setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects cd /media/data/analysis/FREESURFER_TEST/Project /home/ivan/freesurfer/fsfast/bin/register-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC 2011 x86_64 GNU/Linux Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 ---------------- Thu Jan 12 12:51:13 GMT 2012 Run: 001 ---------------- Thu Jan 12 12:51:14 GMT 2012 Update not needed Run: 002 ---------------- Thu Jan 12 12:51:14 GMT 2012 Update not needed Thu Jan 12 12:51:14 GMT 2012 register-sess completed Sess01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /media/data/analysis/FREESURFER_TEST/Project/Sess01 RunList: 001 002 Sess01 001 Update not needed Sess01 002 Update not needed Thu Jan 12 12:51:14 GMT 2012 mc-sess completed SUCCESSFULLY Sess01 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -hemi lh -nolog -update instem fmcpr outstem fmcpr.sm5.fsaverage.hemi ------------------------------ 1/1 Sess01 1/1 Sess01 001 lh --------- Thu Jan 12 12:51:14 GMT 2012 Sess01 001 Update not needed 1/1 Sess01 002 lh --------- Thu Jan 12 12:51:14 GMT 2012 Sess01 002 Update not needed Thu Jan 12 12:51:14 GMT 2012 rawfunc2surf-sess completed ---------------------------------------- Started at Thu Jan 12 12:51:13 GMT 2012 Ended at Thu Jan 12 12:51:14 GMT 2012 preproc-sess done ------------------------------------------- /media/data/analysis/FREESURFER_TEST/Project/Sess01 Thu Jan 12 12:51:14 GMT 2012 anadir = /media/data/analysis/FREESURFER_TEST/Project/Sess01/bold/verbgen.sm5.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2011 The MathWorks, Inc. R2011b (7.13.0.564) 64-bit (glnxa64) August 13, 2011 Warning: Duplicate directory name: /home/ivan/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# Sess01 ############################### /media/data/analysis/FREESURFER_TEST/Project/Sess01 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/ivan/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/ivan/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/data/analysis/FREESURFER_TEST/Project Extension format = nii.gz Error using basename Too many input arguments. Error in fast_ldanaflac (line 423) nuisregevname = basename(nuisreg,'dat'); % remove .dat Error in fast_selxavg3 (line 53) flac0 = fast_ldanaflac(analysis); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n -- Kind Regards, Ivan Alvarez PhD Student Imaging and Biophysics Unit UCL Institute of Child Health 30 Guildford Street, London, WC1N 1EH

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FA and non_FA group analysis
by Antonella Kis 13 Jan '12

13 Jan '12

Dear Doug, I need some help regarding my FA and non-FA group analysis study. I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register. I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmfit-sim with the option grf as you recommended me some time ago: mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if my FA is increasing or decreasing in controls group versus patients group. I will appreciate any help/suggestion. Thank you. Antonella -

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dcmunpack bug for unconsolidated dicoms
by Steven Lehar 13 Jan '12

13 Jan '12

There is a bug in the new *dcmunpack* that replaces the earlier * unpacksdcmdir* when it is unpacking a "fragmented" dicom directory, i.e. one in which the files were saved to DVD incrementally during the scan, as opposed to dicom files that are saved all at once, after all the scanning is complete. The difference can be seen with a 'du' command, here is a fragmented, dicom "PRL007", compared to a consolidated one "PRL007C" of the same data: $ *du* 166156 ./PRL007/DICOM/11020419/14200000 *unconsolidated* 166160 ./PRL007/DICOM/11020419 5188 ./PRL007/DICOM/11020418/50520000 207448 ./PRL007/DICOM/11020418/57160000 101648 ./PRL007/DICOM/11020418/03040000 502616 ./PRL007/DICOM/11020418/42140000 205384 ./PRL007/DICOM/11020418/17590000 1022288 ./PRL007/DICOM/11020418 1188452 ./PRL007/DICOM 1204460 ./PRL007 1022256 ./PRL007C/DICOM/11020418/03040000 *consolidated* 1022260 ./PRL007C/DICOM/11020418 1022264 ./PRL007C/DICOM 1038264 ./PRL007C When *dcmunpack* unpacks a fragmented dicom, the unpacking *appears* to succeed without errors, but the resulting f.nii file is missing a bunch of acquisitions. Calling dcmunpack on an unconsolidated and consolidated dicom respectively produces the f.nii files below: *unconsolidated*: /space/ficus/4/users/PRL_sessions/*PRL042*/prl_moco/006/f.nii $ ls -l f.nii -rw-rw-r-- 1 slehar harrisgp 125043040 Jan 6 17:04 f.nii *consolidated*: /space/ficus/4/users/PRL_sessions/*PRL042C*/prl_moco/006/f.nii $ ls -l f.nii -rw-rw-r-- 1 slehar harrisgp 201720160 Jan 11 20:48 f.nii Examination with osirix reveals the unconsolidated image to have only 318 acquisitions, the consolidated one has 513 acquisitions. And just FYI, I wrote a script called *consolidate* (see attached) that does the consolidation you see above, after which *dcmunpack* unpacked it without loss of acquisitions. This may be an issue that only affects *us* because we do very long ~20 min. functional scans with hundreds of aquisitions, people with more typical scans may not ever experience this issue, and likewise for people who save their scans all at once at the end. Steve Lehar

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manually labeled brains for segmentation atlas
by Wenger, Elisabeth 13 Jan '12

13 Jan '12

Dear Freesurfer specialists, I'm currently working on a comparison between manual segmentations and freesurfer segmentations of the hippocampus. Therefore i would be very interested in the atlas used for subcortical segmentation. On the wiki i read that the manually labeled brains used to build this atlas are about but not completely the same as the ones in the Desikan atlas, namely 39 manually labeled brains by Rahul Desikan. Could you please provide me with some rough sample descriptives on the brains used in the subcortical segmentation atlas, i.e. Age of subjects, male/female? That would be wonderful! Has this atlas changed in any way between version 4.5 and 5.1? As I am specifically working with the hippocampus segmentations, it would also be very interesting to know what the mean size of the hippocampus in this sample was – do you by any chance have some information on this? Thank you very much for your help! Cheers, Elisabeth

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[freesurfer] How do we know the size of manual drawn ROI
by zhang mingxia 12 Jan '12

12 Jan '12

Dear freesurfer experts, I have drawn a ROI manually. However, there is only vertex information (How many vertices of the ROI). How can i get the size information (mm2) of the ROI. Thank you very much Mingxia

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temporal lobe cut off
by Gibbard, Clare 12 Jan '12

12 Jan '12

Hi, I ran recon-all -all -subjid subjectx on around 40 scans. The registrations and skull strips look fine. However, the white matter and pial surface segmentations miss out the left anterior temporal lobe in most subjects. I tried adding in control points to the left temporal lobe and running recon-all -autorecon2-cp -autorecon3 -subjid subjectx. This helped to fill in the missing areas, but new parts of the right temporal lobe were cut out. I then tried adding in control points to both the left and right temporal lobes, but again new regions of the left temporal lobe were cut out. I think it must be an intensity issue, but I can't see how to fix it. Are you able to give me a work flow to sort this? Here are some screenshots: [X][X]Before control points added: [cid:3abaf95b-5c72-4441-9e12-40d1fd13f01c] After control points added to left and right temporal lobes: [cid:e76a0d57-608a-449a-b7b1-e927de878bda] Thank you. Best wishes, Clare Gibbard

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Re: [Freesurfer] Non_FA Group study
by Antonella Kis 12 Jan '12

12 Jan '12

Dear Bruce, Once again many thanks for helping.I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register. I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if my FA is increasing or decreasing in controls group versus patients group. Please advise me. Thank you. Antonella ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Sent: Wednesday, January 11, 2012 11:40 AM Subject: Re: [Freesurfer] Non_FA Group study Hi Antonella, can you post this type of question to the list so that others can answer? Do you mean a map across space or within each of the tracula fascicles? cheers Bruce On Wed, 11 Jan 2012, Antonella Kis wrote: > Dear Bruce, > > Many thanks for your reply and your help. > > I will be very grateful if you can give some advise on how I can do a > comparison between two groups for my FA data or in other words for FA group > analysis since from the significant map I can only find the p values how can > I see if there is an increase or decrease of the FA values for controls > versus patients? > > > Many thanks, > Antonella > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(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>; > "lzollei(a)nmr.mgh.harvard.edu" <lzollei(a)nmr.mgh.harvard.edu> > Sent: Wednesday, January 11, 2012 11:13 AM > Subject: Re: [Freesurfer] Non_FA Group study > > sure, that should be straightforward. > > cheers > Bruce > On Wed, 11 Jan 2012, Antonella Kis > wrote: > > > > > Dear FS team, > > > > > > Can use my results from the mri_cvs_register to do a non_FA group > analysis, > > more exactly I am interested on the mean diffusivity (adc.nii from > > dt_recon). > > > > > > Since from the significant map I can only find the p values how can I see > if > > there is an increase or decrease of the FA values or how can I do an FA > > comparison between two groups? > > > > Thank you very much for your time and help. > > Antonella > > > > > > > > > > > > > > > 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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watershed error in skull strip routine
by Holden, Timothy 11 Jan '12

11 Jan '12

Hi FS experts, I'm encountering an error in the Skull Strip routine with one brain that the FreeSurferWiki site and FS list don't seem to address. The error message is "mri_watershed Error: indices out of bounds" and results in an exit with errors (I've attached the recon-all.log). If I run "recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas " or "recon-all -skullstrip -clean-bm -no-wsgcaatlas -gcut" on this brian the skull strip routine does finish but very little of the skull is removed and large chunks of the brain are removed in the brainmask file. I've checked the Talairach transform and it looks good but I did notice that the WM in the T1.mgz is not in the 110 range but more like 90. Do you think the problem is in the mri_normalize output and could be correct with control points? Your advice is greatly appreciated. Thanks, Tim Holden {Confidentiality Notice} The materials in this email are private and may contain Protected Healthcare Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ***************************************************** Office Ph# (314) 362-7596 Program Office Ph# (314) 362-7245 Fax# (314) 362-7346 Timothy A. Holden, B.S.E. Research Scientist Cochlear Implant Program http://oto.wustl.edu/implant/ Washington University Medical School Department of Otolaryngology 660 S. Euclid Ave St. Louis, MO 63110-1007 **************************************************** The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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'fsaverage' directory
by swoodman＠nmr.mgh.harvard.edu 11 Jan '12

11 Jan '12

Hi all, We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are : /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons We have been running everything in /R01BTX_recons, so we want this to be the model. I found out that: /autofs/cluster/ablood/1/miriam/SD_recons already has an fsaverage directory The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage -> /usr/local/freesurfer/stable5_1_0/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage -> /usr/local/freesurfer/stable5/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage Not sure if: 1. there is a significant difference between these fsaverages and if we need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons? Thank you! Sandra

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Freesurfer January 2012