Re: [Freesurfer] surfaces and gifti
this should work: mris_convert --combinesurfs ./lh.pial ./rh.pial ./pial.gii notice the output name has ./ in it, to override an old freesurfer-ism of appending a default hemi. also note that .gz is not necessary as gzip is the freesurfer default for gifti. however, freesurfers implementation doesnt support storing all the info in one file. the spec does allow this though, and there might be a way to do it with gifti_tool (but my attempts with -infile and -write_gifti failed). but since the gifti file format is xml, there may a straightforward programmatic way to combine all the independently created gifti data files into one. but lastly, i dont know if any of the other gifti people have combined hemi info. n. On Fri, 2011-12-09 at 05:55 +0100, Satrajit Ghosh wrote: hi all, this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz). a related question. once i have this gifti file how do i get annotations+curvature info also into the file? (the gifti schema supports this right?) essentially i am looking for a way to bundle the surface information into a single gifti container. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...
Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess
Hi Tapsya, I've verified the problem and am working on a fix. doug tap...@nmr.mgh.harvard.edu wrote: Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info file (attached) where the parameters mcstem and nuisreg still point to -per-run (mcstem fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis fails. I have attached the analysis.info file in the email Thank you for your help again! -Tapsya Details: Machine: adapt nmr-dev-env (vs 5.1) preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so siemens -fsd bold -fwhm 5 set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt -stc siemens -force -fsd bold -tpef tpef.txt --- I just ran this co mmand and it completed successfully preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 Is this what you ran? I'm also running it to generate the surfaces now, but it does not seem to be complaining. doug Douglas N Greve wrote: I'm currently running preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 and it seems to be going ok, I won't know until tomorrow whether this is really working or not doug r...@nmr.mgh.harvard.edu wrote: Still no luck. mc-sess is stubbornly using -per-run despite that the preproc-sess requests per-sess. This may be where things get on the wrong track. -Tommi Sorry, what I meant was for you to change the name and then run the stream as usual. doug r...@nmr.mgh.harvard.edu wrote: Done. I also made a backup of the registration. The entire directory at /space/adapt/1/users/raij/AVISI_FSFAST5.1/ is a copy of the actual data residing elsewhere (apart from the Freesurfer recons) so feel free to change anything you need. -Tommi I think I've found the problem, but it's going to be a bit difficult to fix. Can you change the name of your registration file to register.dof6.dat and remove write permissions so that it does not get overwritten? doug r...@nmr.mgh.harvard.edu wrote: Yes we have. It exits with the same error as below. -Tommi Have you tried specifying your regfile with -regfile? doug r...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your help today! I tried running preproc-sess again but it again exits with per-session related errors. However, the errors are different than before so I think the changes you made were a step to the right direction. This time preproc-sess \ -sf subjectname \ -df sessdir \ -mni305 \ -per-session \ -sliceorder siemens \ -fsd bold \ -fwhm 5 \ -surface $SUBJECT lhrh \ -noreg \ # I want to use my manually adjusted bold/register.dof6.dat file (1) mc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (2) stc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (3) rawfunc2surf-sess defaults to -per-run and then expects to find instem fmcpr.siemens (4) ERROR: cannot find /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. Apparently the script looks for the registration file inside the run directory (as it should for per-run analysis) instead of the fsd bold where it should reside for a -per-session analysis. This forces the script to exit. I changed permissions so that you can write in the study directory. For details please see below. Thanks! -Tommi Tapsya on machine avml nmr-dev-env (vs 5.1) cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs setenv SUBJECT avml07 logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log preproc-sess log file $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij setenv FREESURFER_HOME /usr/local/freesurfer/dev setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs Linux avml 2.6.32-131.12.1.el6.x86_64 #1 SMP Mon Sep 26 10:13:43
Re: [Freesurfer] mri_surf2surf error - Return code 254
Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ Freesurfer mailing list Freesurfer@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,
Re: [Freesurfer] dt_recon error
Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly. doug Yuko Yotsumoto wrote: Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat I found the same errors reported to this mailing list, but found no solution. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html In YDTI/YD11A/ folder, I have the following files dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see sWiPMemBlock.alFree. Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer/subjects mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /Users/yuko/Documents/FreeSurfer/subjects cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname Darwin hostname Yukos-iMac.local machine i386 user yuko FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii logyflag 1 X/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat usedti 1 glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A IllCondOK 0 DoFFx 0 Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii Using DTI bValue = 700 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] mri_glmfit-sim error with v5.0
Can you tar up your glmdir and drop it to me? doug Yuko Yotsumoto wrote: Thank you Doug, Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd In stead of making csdCache = /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd it did csdCache = /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd It looks like I failed to tell freesurfer that $subject=fsaverage and $hemi=lh. I changed this line to: set csdCache = $CacheDir/fsaverage/lh/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd and this worked. But I still don't understand why I got the error with mri_glmfit-sim. [ERROR 2] In line 93, anattype is set to volume, but I'm doing surface analysis. set anattype = volume; Changing this to set anattype = surface; worked, but does this mean mri_glmfit-sim is specialized for volume analysis only? Is there a way to change this in the command line not in the original code? Best, Yuko Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the name; and make a backup copy). doug On Nov 23, 2011, at 2:07 PM, yukoyy wrote: Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I have /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd in my directory. It looks like I need to somehow tell freesurfer /fsaverage/lh/, but how? Before mri_glmfit-sim, I did the followings: isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz % - Also, when I did: mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite I got several warnings and errors (full error message pasted at the end of this email): cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii Bus error I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second question --- cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ Wed Nov 23 13:55:01 JST 2011 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 kawabata setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 15.248189 nSimPerJob = 100 1/1 Wed Nov 23 13:55:01 JST 2011 mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C
[Freesurfer] Probabilistic V1 labels to volume
Hi There was a post recently on the mailing list about exporting Probabilistic V1 labels to a volume. I have applied the probabilistic mapping of an individual subject and now have the lh.v1.prob.label I would like to convert this label as a volume, and the function mri_label2vol is a little bit confusing. One important thing here is that I don't want the created volume to be binary. but rather to keep the probabilities of a voxel being on V1. I have tried mri_label2vol --label lh.v1.prob.label --subject $SUBJECT --o lh.v1.prob.label I don't understand why I one should need a register.dat file here or even a template file, as I want to generate a volume in RAS space, from a label which I would think is also in RAS space. As for the template file, should it be orig.mgz? Any suggestions here would be appreciated! Regards Ian Charest ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_glmfit search space = 0
Did the data set change between the two analyses? The KingLab wrote: Hello Doug- In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. middle30.asc lh-Avg-Intercept-middle30.asc --- Does the average middle30.asc differ from zero? 1.000 1.000; lh-Diff-Normal-AD-Intercept-middle30.asc --- Does the average middle30.asc differ between Normal and AD? 1.000 -1.000; ninputs = 188 Checking inputs nframestot = 188 Allocing output nframes = 188 Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 Diagnosis2Normal 2 Diagnosis2AD INFO: gd2mtx_method is dods Reading source surface /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ cwd /Volumes/MacintoshHD2/ADNI-PreProcessed cmdline mri_glmfit --y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf fsaverage lh --label /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label --C /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat --C /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat sysname Darwin hostname b417w74-106.med.utah.edu machine i386 user kinglab FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd labelmask /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label maskinv 0 glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled IllCondOK 0 DoFFx 0 Creating output directory /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat Matrix condition is 1 /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label Found 149955 points in label. Pruning voxels by thr: 0.00 Found 149953 voxels in mask Saving mask to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh search space = 75250.1 DOF = 186 Starting fit and test Fit completed in 0.0740167 minutes Computing spatial AR1 on surface INFO: fwhmFromAR1: Fixing group surface area
Re: [Freesurfer] mri_glmfit search space = 0
Sorry, hit the send before I was ready. I was also going to point out that mri_glmfit will zero-out a voxel unless it finds that all inputs are non-zero (pruning). It looks like it could not find any voxels that met this criterion. doug Douglas N Greve wrote: Did the data set change between the two analyses? The KingLab wrote: Hello Doug- In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. middle30.asc lh-Avg-Intercept-middle30.asc --- Does the average middle30.asc differ from zero? 1.000 1.000; lh-Diff-Normal-AD-Intercept-middle30.asc --- Does the average middle30.asc differ between Normal and AD? 1.000 -1.000; ninputs = 188 Checking inputs nframestot = 188 Allocing output nframes = 188 Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 Diagnosis2Normal 2 Diagnosis2AD INFO: gd2mtx_method is dods Reading source surface /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ cwd /Volumes/MacintoshHD2/ADNI-PreProcessed cmdline mri_glmfit --y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf fsaverage lh --label /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label --C /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat --C /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat sysname Darwin hostname b417w74-106.med.utah.edu machine i386 user kinglab FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd labelmask /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label maskinv 0 glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled IllCondOK 0 DoFFx 0 Creating output directory /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat Matrix condition is 1 /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label Found 149955 points in label. Pruning voxels by thr: 0.00 Found 149953 voxels
Re: [Freesurfer] Contrasts in GLM
Both of those will essentially test the same thing, just with a different sign. FS always computes two-tailed tests and reports both tails, so the sign is only a matter of convention. Assuming the Patient class is first in the FSGD and you want volunteers patients to show up as yellow, then you would use the first contrast. Note that when you go to correct for multiple comparisons, make sure to specify the sign as pos (positive). Also, you should remove the mean from you covariates. doug Linda Zhang wrote: Hi Doug, Our hypothesis is that cortical thickness will be lower in patients than in volunteers, once controlled for gender, age, education, etc. I may remove MMSE as diagnosis of the patient is in part based on the MMSE scores. In that case, I would have 12 regressors, in the order you listed minus the MMSE-slope ones. Should I be using [0 0 -1 1 0 0 0 0 0 0 0 0] or [0 0 1 -1 0 0 0 0 0 0 0 0] to test my hypothesis? Cheers, Linda On 7 December 2011 00:01, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the following meaning: 1. MP-Offset 2. FP-Offset 3. MV-Offset 4. FV-Offset 5-8. Age-Slope 9-12. MMSE-Slope 13-16. Ed-Slope The contrast you list below would then compute the average thickness of the volunteers, probably not what you want. But I'm not sure what contrast you actually want (not clear from see if they affect thickness). Can you be more specific/precise? doug Linda Zhang wrote: Hi Doug, Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks! Cheers, Linda On 5 December 2011 23:10, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard. edu mailto:gr...@nmr.mgh.harvard.edu wrote: Linda Zhang wrote: Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory? From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce? It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast. /home/virtualuser/freesurfer/ subjects/lh.MMSE-AD.thickness. 00.mgh doesn't exist, I'm not sure why... Your mris_preproc failed or you are not in the directory that has this file. doug Cheers, Linda On 3 December 2011 01:26, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard. edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard. edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard. edu mailto:gr...@nmr.mgh.harvard.edu wrote: does /home/virtualuser/freesurfer/ subjects/lh.MMSE-AD.thickness. 00.mgh exist? doug Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial.
Re: [Freesurfer] downsampling white matter surface and converting to .tri
Yea, or leave out the --trgsubject all together or spec fsaverage3 as the target. doug Bruce Fischl wrote: I'll leave this for Doug, but it may be that the target subject has to be fsaverage (which is the only one that is actually an icosahedron) cheers Bruce On Thu, 8 Dec 2011, John Griffiths wrote: Hi Bruce. That seems to help - this command runs with no errors mri_surf2surf --hemi lh --srcsubject CBU070282 --sval-xyz white --trgsubject CBU070282 --trgicoorder 3 --trgsurfval white_trgicoorder3 --tval-xyz But unfortunately the --trgicoorder flag doesn't seem to be doing anything; when I run mris_info on the outputs of this command it says 'nvertices' is the same as the original file, for whatever value of trgicoorder I use. The files are the same size as well. Any idea why this might be happening? Thanks, john On 8 December 2011 14:45, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John try adding --tval-xyz so that it knows you want to write out a surface. cheers Bruce On Thu, 8 Dec 2011, John Griffiths wrote: Dear FS peeps, I am trying to downsample a (white matter) surface with mri_surf2surf. I also want the output in .tri format. First problem is that mri_surf2surf doesn't let me output in .tri format mri_surf2surf --hemi lh --srcsubject subj1 --sval-xyz white --trgsubject subj1 --trgicoorder 4 --trgsurfval subj1_white_downsampled.tri --tfmt tri gives me ERROR: could not determine type of temp_surf_white.tri (that happens with the 'tfmt' flag or not) The command does work when the output is a .gii or .mgh file, but when I then try to convert those files to .tri format with mris_convert I get the error ERROR: MRISread: cannot read surface data from file subj1_white_downsampled.gii! ...which is also the error I get when trying to load the file into freeview as a surface. Any idea what I'm doing wrong here? If there is a better way to convert lh.white into a downsampled .tri file please do tell. Thanks very much, john (p.s. thanks to Dan, Doug, and Bruce for getting me to this point...) 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] run preproc-sess with -nomc
Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] Event-Related design and jitter in stimulus onset
Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model of the HRF (no assumed shape), then I usually advise that you have, in total, as much time spent on fixation (or whatever your null stimulus is) as you have for any other stimulus. You can use optseq to compute the actual schedule. doug SHAHIN NASR wrote: Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...
yes doug Gonzalo Rojas Costa wrote: Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] Event-Related design and jitter in stimulus onset
Thanks Doug. In my experiment, each trial (event) consists of 1 sec stimulus presentation and 5 sec blank interval (TR=2). I have also added a condition with just blank presentation which will be repeated as much as other events. I have used optseq2 commands to generate the trial sequence. But I faced two problem/questions: 1) Using this command, I expected to see a Null event (other than my blank condition) with variable length (irrespective of TR) between other trials. But to my surprise, length of the Null event was always a multiplication of TR. Is that correct? 2) Also, for psdmin psdmax I wasn't sure if they are number of TRs or number of seconds and what is a safe window length when my stimuli are very simple visual objects (and no cognitive task). Once again, thanks for your help. On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model of the HRF (no assumed shape), then I usually advise that you have, in total, as much time spent on fixation (or whatever your null stimulus is) as you have for any other stimulus. You can use optseq to compute the actual schedule. doug SHAHIN NASR wrote: Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_surf2surf error - Return code 254
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.**mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.**mgz --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.**mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_**smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/** CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it
Re: [Freesurfer] Event-Related design and jitter in stimulus onset
What is your command line? SHAHIN NASR wrote: Thanks Doug. In my experiment, each trial (event) consists of 1 sec stimulus presentation and 5 sec blank interval (TR=2). I have also added a condition with just blank presentation which will be repeated as much as other events. I have used optseq2 commands to generate the trial sequence. But I faced two problem/questions: 1) Using this command, I expected to see a Null event (other than my blank condition) with variable length (irrespective of TR) between other trials. But to my surprise, length of the Null event was always a multiplication of TR. Is that correct? 2) Also, for psdmin psdmax I wasn't sure if they are number of TRs or number of seconds and what is a safe window length when my stimuli are very simple visual objects (and no cognitive task). Once again, thanks for your help. On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model of the HRF (no assumed shape), then I usually advise that you have, in total, as much time spent on fixation (or whatever your null stimulus is) as you have for any other stimulus. You can use optseq to compute the actual schedule. doug SHAHIN NASR wrote: Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel: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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glmfit search space = 0
What are these asc files? Is this the input that you are having qdec load? If so, then there is at least one subject that has a 0 value at each vertex. The other 187 subjects may be non-zero. doug KYLE ROLLINS HANSEN wrote: Doug- Thank you for your response. The data set did not change between the two analyses. They both used the loading of the exact same .dat file. I think the error is in setting up and creating the new measures, and something went wrong in the process of creating the new measure entitled middle45.asc while it was done correctly for middle30.asc. That measurement is the only difference between the two analyses. Which file does mri_glmfit read in the case of creating a new measure? When I pull up the new measurement .asc files they look identical and don't have zero values for most of the values. Is there a different file the mri_glmfit command is running that would have those zeros in it? Kyle Hansen University of Utah kyle.rollins.han...@utah.edu From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, December 09, 2011 10:46 AM To: KYLE ROLLINS HANSEN; freesurfer Subject: Re: [Freesurfer] mri_glmfit search space = 0 Sorry, hit the send before I was ready. I was also going to point out that mri_glmfit will zero-out a voxel unless it finds that all inputs are non-zero (pruning). It looks like it could not find any voxels that met this criterion. doug Douglas N Greve wrote: Did the data set change between the two analyses? The KingLab wrote: Hello Doug- In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. middle30.asc lh-Avg-Intercept-middle30.asc --- Does the average middle30.asc differ from zero? 1.000 1.000; lh-Diff-Normal-AD-Intercept-middle30.asc --- Does the average middle30.asc differ between Normal and AD? 1.000 -1.000; ninputs = 188 Checking inputs nframestot = 188 Allocing output nframes = 188 Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 Diagnosis2Normal 2 Diagnosis2AD INFO: gd2mtx_method is dods Reading source surface /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ cwd /Volumes/MacintoshHD2/ADNI-PreProcessed cmdline mri_glmfit --y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf fsaverage lh --label /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label --C
Re: [Freesurfer] Event-Related design and jitter in stimulus onset
By default, optseq uses an internal clock synchronize to the TR (so events can only start on the TR). This can be changed by setting dPSD (eg, to 1). This would allow the NULL events to be multiples of 1 instead of 2. The PSD is specified in seconds. doug SHAHIN NASR wrote: optseq2 --ntp 132 --tr 2 --tsearch 0.5 --ev C1 6 4 --ev C2 6 4 --ev C3 6 4 --ev C4 6 4 --ev C5 6 4 --ev C6 6 4 --ev C7 6 4 --ev C8 6 4 --ev C9 6 4 --ev C10 6 4 --nkeep 10 --psdwin 10 16 --o Opt_Par_2nd On Fri, Dec 9, 2011 at 2:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What is your command line? SHAHIN NASR wrote: Thanks Doug. In my experiment, each trial (event) consists of 1 sec stimulus presentation and 5 sec blank interval (TR=2). I have also added a condition with just blank presentation which will be repeated as much as other events. I have used optseq2 commands to generate the trial sequence. But I faced two problem/questions: 1) Using this command, I expected to see a Null event (other than my blank condition) with variable length (irrespective of TR) between other trials. But to my surprise, length of the Null event was always a multiplication of TR. Is that correct? 2) Also, for psdmin psdmax I wasn't sure if they are number of TRs or number of seconds and what is a safe window length when my stimuli are very simple visual objects (and no cognitive task). Once again, thanks for your help. On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model of the HRF (no assumed shape), then I usually advise that you have, in total, as much time spent on fixation (or whatever your null stimulus is) as you have for any other stimulus. You can use optseq to compute the actual schedule. doug SHAHIN NASR wrote: Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Re: [Freesurfer] mri_surf2surf error - Return code 254
Bruce, do you have a command to reduce the number of vertices? John Griffiths wrote: Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com mailto:j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype=
Re: [Freesurfer] mri_surf2surf error - Return code 254
it won't On Fri, 9 Dec 2011, John Griffiths wrote: Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype
Re: [Freesurfer] mri_surf2surf error - Return code 254
not and keep the topology (there is some decimation that is used in the EEG/MEG inverse stuff, but it's just to generate points, not faces) On Fri, 9 Dec 2011, Douglas N Greve wrote: Bruce, do you have a command to reduce the number of vertices? John Griffiths wrote: Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta,john On 9 December 2011 17:22, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com mailto:j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype=
Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess
OK, I think I've fixed it. I've checked the fix into dev which should be live tomorrow. When you make the analysis, add -per-session to the cmd line. doug Douglas N Greve wrote: Hi Tapsya, I've verified the problem and am working on a fix. doug tap...@nmr.mgh.harvard.edu wrote: Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info file (attached) where the parameters mcstem and nuisreg still point to -per-run (mcstem fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis fails. I have attached the analysis.info file in the email Thank you for your help again! -Tapsya Details: Machine: adapt nmr-dev-env (vs 5.1) preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so siemens -fsd bold -fwhm 5 set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt -stc siemens -force -fsd bold -tpef tpef.txt --- I just ran this co mmand and it completed successfully preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 Is this what you ran? I'm also running it to generate the surfaces now, but it does not seem to be complaining. doug Douglas N Greve wrote: I'm currently running preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 and it seems to be going ok, I won't know until tomorrow whether this is really working or not doug r...@nmr.mgh.harvard.edu wrote: Still no luck. mc-sess is stubbornly using -per-run despite that the preproc-sess requests per-sess. This may be where things get on the wrong track. -Tommi Sorry, what I meant was for you to change the name and then run the stream as usual. doug r...@nmr.mgh.harvard.edu wrote: Done. I also made a backup of the registration. The entire directory at /space/adapt/1/users/raij/AVISI_FSFAST5.1/ is a copy of the actual data residing elsewhere (apart from the Freesurfer recons) so feel free to change anything you need. -Tommi I think I've found the problem, but it's going to be a bit difficult to fix. Can you change the name of your registration file to register.dof6.dat and remove write permissions so that it does not get overwritten? doug r...@nmr.mgh.harvard.edu wrote: Yes we have. It exits with the same error as below. -Tommi Have you tried specifying your regfile with -regfile? doug r...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your help today! I tried running preproc-sess again but it again exits with per-session related errors. However, the errors are different than before so I think the changes you made were a step to the right direction. This time preproc-sess \ -sf subjectname \ -df sessdir \ -mni305 \ -per-session \ -sliceorder siemens \ -fsd bold \ -fwhm 5 \ -surface $SUBJECT lhrh \ -noreg \ # I want to use my manually adjusted bold/register.dof6.dat file (1) mc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (2) stc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (3) rawfunc2surf-sess defaults to -per-run and then expects to find instem fmcpr.siemens (4) ERROR: cannot find /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. Apparently the script looks for the registration file inside the run directory (as it should for per-run analysis) instead of the fsd bold where it should reside for a -per-session analysis. This forces the script to exit. I changed permissions so that you can write in the study directory. For details please see below. Thanks! -Tommi Tapsya on machine avml nmr-dev-env (vs 5.1) cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs setenv SUBJECT avml07 logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log preproc-sess log file $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij setenv FREESURFER_HOME
Re: [Freesurfer] tcl script question: labl_set_color
OK, right-clicking on the surface did in fact de-select the label (turning it all to a uniform color). Way to script a right-click? (I see left click...) Now that this is more or less working, I am looking to do something slightly different: i.e., combine the boundaries of one set of regions, one highlighed region, and an activation map. Is there a way to fill just one label and leave outlines for a different set of labels in the same image? Or alternatively set a different outline color for one label? As in my previous post, I am looking to do this via tcl script if possible. Thanks. On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: yes, just use the -tcl script name option, but don't but an exit command at the end of the tcl script cheers Bruce On Mon, 5 Dec 2011, Justin Baker wrote: Ah - in that case I have a total newbie question, since I primarily use tksurfer via command line: Is there a way to load up a case using the tcl script, but then leave it open rather than quit? This way I could try de-selecting with right-click. Thanks. On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think so, but I want to see if it fixes your problem before I go digging through the tcl code to see what it is On Mon, 5 Dec 2011, Justin Baker wrote: Is there a command to do this via tcl script? Justin On Sun, Dec 4, 2011 at 8:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What happens if you right click on the surface then? On Dec 4, 2011, at 8:17 PM, Justin Baker justintba...@gmail.com wrote: Hi Bruce, Thanks. Some progress! That resulted in the label border turning red, but the fill is still white. Any other thoughts? Cheers, Justin On Wed, Nov 30, 2011 at 2:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Justin try unselecting the label with: labl_select -1 cheers Bruce On Wed, 30 Nov 2011, Justin Baker wrote: I am trying to use tksurfer to script overlay of a label + functional map onto an fsaverage5 surface. In particular, I want to set the label to fill and color it red. I have: set labelstyle 0 labl_set_color 0 255 0 0 As you can see below, the output of label_print_list shows that the color of the label should be 255 0 0 but it looks white in the output image. Am I missing something? Thanks subject is fsaverage5 hemiis lh surface is inflated Label 0 Name: lh.17Networks_LH_ContB_PFClv.**label, 109 vertices Structure: -1 Color: 255 0 0 Visible: 1 Bounds: x -20.879234 12.792567 y -4.00 109.853737 z -4.033233 4.040778 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/**compliancelinehttp://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. ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] tcl script question: labl_set_color
I think you can set the outline color of each label indepently by using it's index which is assigned in the order in which it is loaded I believe. So in our example below labl_set_color 0 255 0 0, change the first 0 to a 1 for the second label. Also, I would have thought labl_select -1 would deselect the label and turn off the white marks, but if not you can also try calling clear_all_vertex_marks in the tcl script On Fri, 9 Dec 2011, Justin Baker wrote: OK, right-clicking on the surface did in fact de-select the label (turning it all to a uniform color). Way to script a right-click? (I see left click...) Now that this is more or less working, I am looking to do something slightly different: i.e., combine the boundaries of one set of regions, one highlighed region, and an activation map. Is there a way to fill just one label and leave outlines for a different set of labels in the same image? Or alternatively set a different outline color for one label? As in my previous post, I am looking to do this via tcl script if possible. Thanks. On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, just use the -tcl script name option, but don't but an exit command at the end of the tcl script cheers Bruce On Mon, 5 Dec 2011, Justin Baker wrote: Ah - in that case I have a total newbie question, since I primarily use tksurfer via command line: Is there a way to load up a case using the tcl script, but then leave it open rather than quit? This way I could try de-selecting with right-click. Thanks. On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think so, but I want to see if it fixes your problem before I go digging through the tcl code to see what it is On Mon, 5 Dec 2011, Justin Baker wrote: Is there a command to do this via tcl script? Justin On Sun, Dec 4, 2011 at 8:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What happens if you right click on the surface then? On Dec 4, 2011, at 8:17 PM, Justin Baker justintba...@gmail.com wrote: Hi Bruce, Thanks. Some progress! That resulted in the label border turning red, but the fill is still white. Any other thoughts? Cheers, Justin On Wed, Nov 30, 2011 at 2:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Justin try unselecting the label with: labl_select -1 cheers Bruce On Wed, 30 Nov 2011, Justin Baker wrote: I am trying to use tksurfer to script overlay of a label + functional map onto an fsaverage5 surface. In particular, I want to set the label to fill and color it red. I have: set labelstyle 0 labl_set_color 0 255 0 0 As you can see below, the output of label_print_list shows that the color of the label should be 255 0 0 but it looks white in the output image. Am I missing something? Thanks subject is fsaverage5 hemi is lh surface is inflated Label 0 Name: lh.17Networks_LH_ContB_PFClv.label, 109 vertices Structure: -1
[Freesurfer] extracting time courses from fMRI
Hi All, I'm trying to extract time courses from functional data I started by registering my motion corrected functional data to my segmentation using bbregister, then I used: mri_vol2surf --src Motioncorrectedfunctional.nii.gz --srcreg register.dat --out suface.mgz —hemi rh mri_segstats --in surface.mgz --annot subject rh aparc --sum sum_output --avgwf Timecourse_output Is this a sensible thing to do? I'm not particually sure about the mri_vol2surf step.. Thanks in advance. Pete ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] extracting time courses from fMRI
yes, that is the correct procedure. doug Hellyer, Peter wrote: Hi All, I'm trying to extract time courses from functional data I started by registering my motion corrected functional data to my segmentation using bbregister, then I used: mri_vol2surf --src Motioncorrectedfunctional.nii.gz --srcreg register.dat --out suface.mgz —hemi rh mri_segstats --in surface.mgz --annot subject rh aparc --sum sum_output --avgwf Timecourse_output Is this a sensible thing to do? I'm not particually sure about the mri_vol2surf step.. Thanks in advance. Pete ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] dt_recon error
Hi Doug, Thank you for your reply. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line I don't quite understand how --b works with dt_recon. I did: dt_recon --i /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A and it stopped after creating dwi.nii and dwi-ec.nii. I thought dt_recon is the command to compute bvals and bvecs. How do I supply bvecs and bvals on the command line? Yuko On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote: Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly. doug Yuko Yotsumoto wrote: Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat I found the same errors reported to this mailing list, but found no solution. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html In YDTI/YD11A/ folder, I have the following files dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see sWiPMemBlock.alFree. Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer/subjects mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /Users/yuko/Documents/FreeSurfer/subjects cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname Darwin hostname Yukos-iMac.local machine i386 user yuko FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii logyflag 1 X/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat usedti 1 glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A IllCondOK 0 DoFFx 0 Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii Using DTI bValue = 700 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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. \ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] dt_recon error
Hi Yuko, it will get the bvals and bvecs from a set of tables distributed with FS. But the dicom has to have some information in it that tells it which table to use. It looks like your dicom did not have this information (it is not in the info dump created from the dicom). So you'll have to create text files of the bval/bvecs. The expected format is given in the help. You'll have to ask someone who knows about your sequences as to what the actual values you should use. doug On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: Hi Doug, Thank you for your reply. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line I don't quite understand how --b works with dt_recon. I did: dt_recon --i /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A and it stopped after creating dwi.nii and dwi-ec.nii. I thought dt_recon is the command to compute bvals and bvecs. How do I supply bvecs and bvals on the command line? Yuko On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote: Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly. doug Yuko Yotsumoto wrote: Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat I found the same errors reported to this mailing list, but found no solution. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html In YDTI/YD11A/ folder, I have the following files dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see sWiPMemBlock.alFree. Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer/subjects mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /Users/yuko/Documents/FreeSurfer/subjects cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname Darwin hostname Yukos-iMac.local machine i386 user yuko FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii logyflag 1 X/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat usedti 1 glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A IllCondOK 0 DoFFx 0 Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii Using DTI bValue = 700 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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. \ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
