Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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trac-all -path error
by Chris Watson 07 May '12

07 May '12

Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. ------------------------------------------------------------------------ Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms

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Comparing Cortical Thickness
by Jeff Sadino 03 May '12

03 May '12

Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino

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OBJ conversion
by Darshan P 03 May '12

03 May '12

Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan

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Cortical Normalization Questions
by Jeff Sadino 23 Apr '12

23 Apr '12

Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html) Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff

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Longitudinal Template Edits
by Tate, David Franklin 09 Apr '12

09 Apr '12

We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion. Our template results have several areas that concern us and we are wondering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they seem to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editing tool to use in tkmedit and if there are any configuration changes needed). We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure. Any help would be greatly appreciated. Thanks, [cid:3A68F9FB-CA43-46B6-8D1B-8F0F42243677@v3.uthscsa.edu] [cid:4483FB3B-AB38-4350-973B-A800BD6FD3CA@v3.uthscsa.edu] [cid:220E38D7-5796-47E4-BDE5-DDB75CB6E2AE@v3.uthscsa.edu]

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mri_label2vol cannot allocate memory
by Anthony Dick 06 Apr '12

06 Apr '12

Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader > chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick

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aseg.mgz looks worse after longitudinal processing on 5.1
by Brain Apprentice 05 Apr '12

05 Apr '12

Hi Surfers, I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good after the Longitudinal Processing, the aseg segmentation for each subject is often looking much worse. I have attached a sample screen grab to show you what I mean. The images on top show the Longitudinal Processed views. The images on bottom are of the same subject before the Longitudinal Processing has occurred. It is possible I am doing something wrong. I just thought I would throw it out to the experts to see if they are having similar experiences or if there are suggestions on things that I should do. Thanks very much, B.A.

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Error on Step 3 of longitudinally process
by Brain Apprentice 05 Apr '12

05 Apr '12

Hi, I was wondering if I am doing something wrong when doing step 3 of the longitudinally process. The error I get is: ERROR: Template/base ID cannot be the same as a time point ID (in /shared/subjects/subjects/a-aut-v510/10022/base-tps) Here is the environment: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer510 FSFAST_HOME /usr/local/freesurfer510/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer510/subjects MNI_DIR /usr/local/freesurfer510/mni FSL_DIR /usr/local/fsl418 ---------- FreeSurfer variables reset ---------- SUBJECTS_DIR /shared/subjects/subjects/a-aut-v510 FSLOUTPUTTYPE NIFTI_GZ The command I am running is: recon-all -long 10022--01-24-06--0470 10022 -all The base-tps file is: 10022--01-24-06--0470 10022--03-14-06--0441 10022--04-14-08--0463 10022--04-25-06--0442 10022--07-25-06--0462 10022--08-26-10--0555 10022--10-21-06--0461 10022--11-20-08--0412 The <tpNid> is: 10022--01-24-06--0470 The <templateid> is: 10022 I am trying to follow the format listed on http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing however it still does not seem to work. Does anyone have any idea on what I need to do differently? Thank You in advance for any suggestions you might have. B.A.

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Qdec issue
by sonya kaur 05 Apr '12

05 Apr '12

Hi everyone, I realize I'm quickly becoming an annoyance, but I'm having trouble loading my data file into qdec. I keep getting the error: QdecDataTable::Load failed to tokenize string: on line 88 of HTN_FMRI_Qdec. HTN_FMRI_Qdec is the name of my data file. I do not even have a line 88 as I have only 86 subjects and 4 variables. Thank you! Sonya -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E <sonya_kaur(a)mail.utexas.edu> sonya_kaur(a)mail.utexas.edu

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Freesurfer March 2012