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Poor Cortical Reconstructions in Pediatrics
by Xin Zhang 10 May '12

10 May '12

Hello FreeSurfers, Please ignore the previous email. This one includes an example picture. We are processing about 100 pediatric subjects ages 3-9 using FreeSurfer 5.1.0. For some reason, in about 25 of the subject, the right supramarginal, right middletemporal, and superiortemporal regions have poor cortical reconstructions. After reviewing the raw scans, we do not see any reason why these regions would be poorly segmentated. Can anyone give us any feedback for why these regions are reconstructing poorly? Our only ideas are that our subject ages might be causing issues, or normalizing the minor brightness gradient could be causing issues (although the poor segmentations occur even on subjects that have no brightness gradient on their raw scans). Thank you very much, Xin

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Qdec 1.4 Error
by Kairys, Anson 10 May '12

10 May '12

Hi everyone, I ran recon-all and –qcache ran successfully as well. Now I am getting this error in qdec v1.4 when I try to “generate stats data table” (see attached) I also attached one subjects aseg.stats file if that helps. I remember seeing another error indicating (file too small, but I think my $SUBJECTS_DIR was not set correctly that time. Qdec.table.dat loaded in fine, but it seems I am missing some files? Any suggestions? Best wishes Anson K. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: [Freesurfer] optseq2 and tnullmin/max
by Hanah Chapman 10 May '12

10 May '12

Hi Doug, Thank you for the quick response. I tried the new file, and it fixes the problem with the tnullmax. However, I'm still having trouble computing the right number of tp. If I want a null after every event, that's 96 nulls. If I set the tnullmax/min range at 4-10s, then nulls will have an average duration of 7s, so 96 * 7/2 = 336 tp, plus 96 tp for the stimuli, = 432 tp. But with 432 tp I get a "could not enforce tnullmax" error. Oddly, with a lower ntp (384), I don't get an error, but get extra time at the end (so one null at the end of 70s). Evidently I'm not computing the ntp correctly. Alternatively, could I just cut the final null even down to the right length? Thanks again, Hanah > Hi Hanah, I just found and fixed the bug. It was making the effective > tNullMax = tNullMin + your specified tNullMax. I've put a new (linux) > version here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux > doug > > > On 05/09/2012 06:09 PM, Chapman, Hanah wrote: > > Dear list, > > > > I have an optseq2 question, and would very much appreciate your time. > > > > I'm having difficulty calculating the required number of timepoints. > > I'd like to use --tnullmin and --tnullmax so as to have a null event > > in between each trial, with a duration of 4-8 sec. I have 16 > > conditions, 6 repeats/run, 2s trials, 2s TR. I computed that a run > > would need 16*6 = 96 timepoints for the trials. Then there would be 96 > > null events (to have one between each trial), so with an average 6s > > duration for nulls, a run needs 96*6/2 = 288 timepoints for the nulls, > > so 96+288 = 384 tp total. However, when I run optseq2 with these > > parameters, I still get nulls that are longer than 8s, and there is > > evidently extra time left over, since the last null event is 70 sec > > long. I'm using the following code: > > > > --ntp 384 --tr 2 --psdwin 0 20 --tnullmin 4 --tnullmax 8 --nkeep 6 > > --o outfile --nsearch 1000 \ > > --ev DD 2 6 \ > > --ev DF 2 6 \ > > --ev DP 2 6 \ > > --ev DN 2 6 \ > > --ev FF 2 6 \ > > --ev FD 2 6 \ > > --ev FN 2 6 \ > > --ev FP 2 6 \ > > --ev PP 2 6 \ > > --ev PD 2 6 \ > > --ev PN 2 6 \ > > --ev PF 2 6 \ > > --ev NN 2 6 \ > > --ev ND 2 6 \ > > --ev NF 2 6 \ > > --ev NP 2 6 > > > > I understand that the 4-8s range may be too tight, and relaxing it is > > not a big deal. However, I tried 4-10s, and still has the problems > > with nulls > 10s and extra time at the end. > > > > Thank you for your time, > > > > Hanah Chapman > > Postdoctoral Fellow > > The Ohio State University > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA niftii file
by Gabor Perlaki 10 May '12

10 May '12

Dear all, Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think TRACULA needs the bvecs in the image coordinate system, which is not the same as scanner coordinate system in case of oblique acquisition. Do I need to use dcm2nii with correction for slice angulation to compensate for the image plane. The DTI was acquired on a Simenes TRIO with the standard Siemens DTI sequence (ep2diff), not the MGH DTI sequence. Software version: VB17A Does anybody have any experience with TRACULA and Siemens DTI? Thanks, Gabor

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Re: [Freesurfer] Error with recon-all
by Ed Gronenschild 10 May '12

10 May '12

Hi Nick, Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore. Cheers, Ed On 9 May 2012, at 18:53, Nick Schmansky wrote: > can you send the recon-all.log file? does it say why the > lh.orig_corrected file wasnt created? > > On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote: >> Hi, >> >> I'm using the version of recon-all that Nick provided >> at April 17 to be able to run nu_correct prior to the >> Talairach stage. (I'm on a Mac, OSX 10.6, version >> v5.1.0). The command given was >> >> recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ >> -clean-tal -s subject. >> >> recon-all stopped and issued the following error: >> >> cp: ../surf/lh.orig_corrected: No such file or directory. >> >> Note that I included the option -no-wsgcaatlas to get >> a better skullstripping because in the default mode >> the skulltripping was bad. With this option it looks >> good. >> I got the above error regularly for other subjects as well >> and by including the -no-wsgcaatlas option recon-all >> finished without error, except for the present case. >> >> Cheers, >> Ed >> _______________________________________________ >> 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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recon-all error
by Rashmi Singh 09 May '12

09 May '12

Hello, I ran recon –all on my scans and the output files reported the following error: SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage/label/lh.BA1.label Linux dale 2.6.32-40-server #87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012 x86_64 GNU/Linux recon-all -s AA435.C1 exited with ERRORS at Wed May 9 01:37:19 CDT 2012. I couldn't locate the folder fsaverage: /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage Please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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optseq2 and tnullmin/max
by Chapman, Hanah 09 May '12

09 May '12

Dear list, I have an optseq2 question, and would very much appreciate your time. I'm having difficulty calculating the required number of timepoints. I'd like to use --tnullmin and --tnullmax so as to have a null event in between each trial, with a duration of 4-8 sec. I have 16 conditions, 6 repeats/run, 2s trials, 2s TR. I computed that a run would need 16*6 = 96 timepoints for the trials. Then there would be 96 null events (to have one between each trial), so with an average 6s duration for nulls, a run needs 96*6/2 = 288 timepoints for the nulls, so 96+288 = 384 tp total. However, when I run optseq2 with these parameters, I still get nulls that are longer than 8s, and there is evidently extra time left over, since the last null event is 70 sec long. I'm using the following code: --ntp 384 --tr 2 --psdwin 0 20 --tnullmin 4 --tnullmax 8 --nkeep 6 --o outfile --nsearch 1000 \ --ev DD 2 6 \ --ev DF 2 6 \ --ev DP 2 6 \ --ev DN 2 6 \ --ev FF 2 6 \ --ev FD 2 6 \ --ev FN 2 6 \ --ev FP 2 6 \ --ev PP 2 6 \ --ev PD 2 6 \ --ev PN 2 6 \ --ev PF 2 6 \ --ev NN 2 6 \ --ev ND 2 6 \ --ev NF 2 6 \ --ev NP 2 6 I understand that the 4-8s range may be too tight, and relaxing it is not a big deal. However, I tried 4-10s, and still has the problems with nulls > 10s and extra time at the end. Thank you for your time, Hanah Chapman Postdoctoral Fellow The Ohio State University

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longitudinal study in counterbalance design
by lordowen 09 May '12

09 May '12

Hi all: We performed a thickness change study which related to the menstrual cycle. We scanned subjects during different menstrual phases in a counterbalance manner. Thus when we conduct a longitudinal analysis, we need to set time point according to the actual scanning order (i.e., 1st scan as Tp1 and so on) or according to the phase (i.e., menstruation phase as Tp1 and other phase as TpN)? Thanks for your suggestion. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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file format of patch file (?h.full.patch.3d )
by Cris Lanting 09 May '12

09 May '12

Dear all, I'm trying to access and read a binary patch file (like ?h.full.patch.3d) rather than a converted ascii file. I've found a description of the lay-out of such a file at http://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats that in turn links to http://wideman-one.com/gw/brain/fs/surfacefileformats.htm: Patch File -Binary *Location (byte)* *Item* *Types* *Comment* 0 PointCount Int4 Count of points to follow (Updated 2003-07-06) ? + ?n vtx x y z Int4, Int2, Int2, Int2 vtx is special: (mris->vertices[k].border)?-(k+1):k+1; See below for explanation (Updated 2003-07-06) However, things may have changes over time and I was wondering whether the lay-out is still the same. It would really help if someone could indicate the (correct) order, type and size of the bytes in the binary patch file. I.e., it seems to start with a count of the number of vertices that constitute the patch (int4), followed by a vertex-index (int4), and the coordinates (x,y,z; each int2) for each of the vertices. What I don't know is how many bytes (and their type) are used to code each of those elements. Note that the description of the w-files (the output of mri_vol2surf) seems to be ok: W ("Weight") Format *Location (byte)* *Item* *Type* *Comment* 0 Latency Int2 2 Count Int3 Count of vertex-value pairs to follow 5 + 7n VertexNum Int3 5 + 7n + 3 VertexVal Float4 mris_convert uses %f I can read those in easily (although I have no idea what latency means...): Thanks! Cris Cris Lanting, PhD MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD Phone: +44 - (0)115 9223431 cris(a)ihr.mrc.ac.uk <ana(a)ihr.mrc.ac.uk>

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Entorhinal Cortex
by Alan Francis 09 May '12

09 May '12

Hi Imagers: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston

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