[Freesurfer] recon-all error
Dear freesurfer experts, I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1 #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3(det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help will be appreaciated, Many thanks in advance Rafa ___ 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] Postdoctoral Fellow - University of Oslo
A three-year term position as Postdoctoral Fellow (governmental position code 1352) is available at the Norwegian Centre for Mental Disorders Research (NORMENT) and the KG Jebsen Centre for Psychosis Research – TOP Study Group, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Norway. http://uio.easycruit.com/vacancy/983405/70331?iso=no ** Job Description NORMENT coordinates a translational multicenter study involving all psychiatric hospital departments in Oslo and several research groups at the University of Oslo. The main purpose of the research is to disentangle and characterize the neurobiological, genetic, psychological and environmental factors contributing to the development of severe mental disorders. Through our extensive infrastructure for clinical evaluations, neuropsychological testing, MRI brain imaging and biobanking we are assembling a comprehensive database comprising genetic and brain imaging data from a large number of healthy controls and patients suffering from psychotic disorders including schizophrenia and bipolar disorders. The postdoctoral fellow will play a central role in the analysis and dissemination of data from this large imaging genetics database. The research will be carried out as part of a cross-disciplinary team of researchers in the Multimodal Imaging and Biostatistics groups at NORMENT in close collaboration with researchers at the University of California San Diego and deCODE Genetics. ** We offer An ambitious and exciting research environment with a strong multidisciplinary profile and excellent opportunities for academic development at NORMENT, which was recently granted Centre of Excellence Status by the Research Council of Norway. A postdoctoral position in Norway is equivalent to the US position of assistant professor and is intended to prepare and qualify talented candidates for a research career. Salary is in the range between ltr 57 and ltr 65, i.e. from NOK 473 400 to NOK 548 700, depending on qualifications. Pension and national health insurance is included in addition to several attractive welfare arrangements (http://www.uio.no/english/for-employees/employment/welfare). ** Qualifications The ideal candidate is ambitious and highly motivated for pursuing a career in science, hold a PhD in neuroimaging, computational neuroscience, biomedical engineering, cognitive neuroscience, or equivalent, have a strong background and interest in neuroscience, MRI analysis and statistics, and an excellent publication record. Candidates with a strong interest in and experience with methods for integrating multimodal imaging measures, including structural MRI, diffusion tensor imaging (DTI), and functional MRI, are in particular encouraged to apply. Experience with imaging genetics is an advantage. ** The application Applications are submitted through the University online recruitment system and must include application letter including motivation for applying for the position, CV summarizing education, relevant work experience, grants etc, a complete list of publications and academic work, and contact details of 2-3 references. Application deadline: June 30 2013. After the initial screening process, short-listed candidates may be asked to submit selected publications, educational certificates and transcripts of records. Interviews may be included as part of the selection process. For any informal enquiries regarding the position, please contact professor Ole A. Andreassen (o.a.andreas...@medisin.uio.no) and associate professor Lars T. Westlye (l.t.west...@psykologi.uio.no). http://uio.easycruit.com/vacancy/983405/70331?iso=no ___ 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] Surface area measurement method
Hello FreeSurfers, after reading this [1] paper about measuring surface area, i realized i don't know what the default way of measuring surface area is in FreeSurfer. Is it similar to what's described in the paper? Could you point me to the right documentation or publication? Forgive me if i've overlooked it, i found something for thickness, but not for area. To clarify, i don't mean parcellation-based areas, i mean the measure that i find in /surf/hemi.area. thanks, regards, Andreas [1] Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43 ___ 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] first level glm analysis on surface space
Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take each functional volume corresponding to each TR and move each volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). Then I want to run first level glm on the data like its done for volume data in spm, fsl, afni etc. My question is are there tools in freesurfer to do this on surfaces ? If not, can the mgh file be converted to a gifti file and maybe it can be used to make first level glms in afni, spm or fsl ? I will really appreciate your opinion about this. Thank you very much, Subha ___ 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] mri_mc vs. recon-all surfaces
Dear all, I need to extract three surfaces from MRI data: - GM-WM interface - thus, lh.white and rh.white would be the answer. - Pial interface - thus, lh.pial + rh.pial - CSF surface For CSF, as far as I know, the best option would be to generate a binary volume merging the appropriate labels from aseg.mgz. Then use mri_mc to obtain the surface, right? For white and pial I guess the best option would be to use the recon-all outcome, but I have two questions: * Is there any mean to merge both hemispheres? I've tried several methods but I get trouble with the consistency of the cells... the points are aggregated, but no work is done to merge cells and remove points. * What are the differences between the recon-all outcome (lh.pial,rh.pial,lh.white,rh.white) with respect obtaining masks from aseg.mgz and then mri_mc? Thank you so much Best regards, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland ___ 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] hippocampal subfield segmentation
Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ 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] error in 5.3
Hi Robert I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2 cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote: Hi, We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following: export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3 It ran for about 4.5 hours and then gave this error: --- [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with thresh in their name under that subject. Thanks! -Robert ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ 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] Parameterization Optseq
Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out? Our task consists of 3 runs of 72 trails each, in which participants are presented with a fixation cross that remains on the screen for a fixed duration of 1 sec, followed by one out of nine different stimuli that remains on the screen for a fixed duration of 4 sec. This gives a scan duration of 360 sec. We would then like to add 25% jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this results in 225 time points. However, Optseq yields an error if ntp is set to 225, ev duration set to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 ERROR: could not enforce tNullMax=6 (ntries=10) You will need to reduce the number of time points or increase the number of presentations. However, reducing the number of time points makes Optseq to only insert null events of 1.0 or rarely 2.0 sec without much variation. Optimization with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and tnullmax to 6.0 does work. However, this renders Optseq to insert null events of a fixed duration op 1.0 sec, which is not what we want. Could you please advise us in how to set these parameters? Thank you in advance. Best regards, Laura Dekkers -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekk...@gmail.com ___ 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] recon-all error
Hi Rafa that sounds like a bug. Can you gzip and upload the whole subject dir? cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote: Dear freesurfer experts, I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1 #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help will be appreaciated, Many thanks in advance Rafa ___ 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_mc vs. recon-all surfaces
Hi Oscar what do you mean by the CSF surface? Outside the brain or in the ventricles? If outside, there is some code for creating boundary element models for EEG/MEG analysis. There is no trivial way to create a single surface. The way I've done it in the past is to replace the lh or rh values in the filled.mgz with the other one and go from there, but it's not meant to work that way and you have to mess with it a fair amount. cheers Bruce On Tue, 4 Jun 2013, Oscar Esteban wrote: Dear all, I need to extract three surfaces from MRI data: - GM-WM interface - thus, lh.white and rh.white would be the answer. - Pial interface - thus, lh.pial + rh.pial - CSF surface For CSF, as far as I know, the best option would be to generate a binary volume merging the appropriate labels from aseg.mgz. Then use mri_mc to obtain the surface, right? For white and pial I guess the best option would be to use the recon-all outcome, but I have two questions: * Is there any mean to merge both hemispheres? I've tried several methods but I get trouble with the consistency of the cells... the points are aggregated, but no work is done to merge cells and remove points. * What are the differences between the recon-all outcome (lh.pial,rh.pial,lh.white,rh.white) with respect obtaining masks from aseg.mgz and then mri_mc? Thank you so much Best regards, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland ___ 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
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote: Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.00 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLowCWPHi NVtxs Annot ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] error with trying 5.3 on 5.2 data for autorecon2 and autorecon3, balabel throwing error.
Hi all,
In our efforts to take our 5.2 edits to 5.3 we tried the command below (in the
attached thread), but we also tried the command
recon-all –s [subject-d] -autorecon2 –autorecon3
and those jobs are also running for some time but then crashing with the same
error complaining that lh.BA1.thresh.label does not exist.
We are on RedHat 5.2, running the 2.6.18-19.1.13.e15 kernel and using the BASH
environment. We are using the release 5.3.0-centos04.
The log and other relevant files can be found at:
http://www-personal.umich.edu/~rcwelsh/bug/recon-all.cmd
http://www-personal.umich.edu/~rcwelsh/bug/recon-all.log
http://www-personal.umich.edu/~rcwelsh/bug/recon-all.env
http://www-personal.umich.edu/~rcwelsh/bug/recon-all.error
I've dug into the code and see that the block of code in recon-all was
introduced going from 5.2 to 5.3.
# generate .thresh labels
foreach balabel (BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 V1 V2 MT)
set cmd=(mri_label2label \
--srcsubject fsaverage \
--srclabel
$SUBJECTS_DIR/fsaverage/label/${hemi}.${balabel}.thresh.label \
--trgsubject $subjid \
--trglabel ./${hemi}.${balabel}.thresh.label \
--hemi ${hemi} \
--regmethod surface)
echo \n $cmd \n| tee -a $LF | tee -a $CF
if($RunIt) $fs_time $cmd | tee -a $LF
if($status) goto error_exit;
end # balabel
This is what is throwing the error.
Hopefully, we can get this resolved soon.
(Also as a side note in the version 5.2 we had to comment out the reference to
perirhinal in the first foreach balabel loop as perirhinal was giving a bug)
Thanks,
-Robert
**
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] error in 5.3
ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those. thanks -robert On 6/4/13 8:59 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Robert I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2 cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote: Hi, We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following: export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3 It ran for about 4.5 hours and then gave this error: -- - [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh. label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- - Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with thresh in their name under that subject. Thanks! -Robert ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 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. ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error in 5.3
hi bruce, thanks. from the reading of recon-all it looks like this is a failure is occurring in the latter part of autorecon3 so I'm just rerunning that set and skipping autorecon2 on the subjects that failed. correct? best, -robert On 6/4/13 9:38 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: p.s. you can check to see if those labels exist in your fsaverage/label dir On Tue, 4 Jun 2013, Welsh, Robert wrote: ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those. thanks -robert On 6/4/13 8:59 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Robert I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2 cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote: Hi, We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following: export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3 It ran for about 4.5 hours and then gave this error: - - - [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh . label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - - - Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with thresh in their name under that subject. Thanks! -Robert ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 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. ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfield segmentation
I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] Fwd: [All] freesurfer and centos6 updates!
Hi all, I would like to save copy of the CentOS5 release of Freesurfer in my group's work space as described in the email below. The link in the email that is supposed to explain this doesn't work; could someone please let me know how to do this or point me to another webpage that explains it? Thanks! Emily Begin forwarded message: From: Nick Schmansky ni...@nmr.mgh.harvard.edu Subject: [All] freesurfer and centos6 updates! Date: December 10, 2012 4:08:30 PM EST To: a...@nmr.mgh.harvard.edu Cc: Martinos-tech martinos-t...@yahoogroups.com, Help h...@nmr.mgh.harvard.edu WARNING! The default Freesurfer version that runs on CentOS6 machines is going to change next Monday the 17th to a new CentOS6 specific version. Right now at the Martinos Center we have a mix of CentOS4, CentOS5 and CentOS6 machines at the center. All these currently use a version of freesurfer built on CentOS4 for maximum compatibility. However, this means those users with CentOS6 systems are using a version that is slower than they could be using if properly optimized. It is time for users of CentOS6 system to no longer be held back by the older systems. So on next Monday the 17th, the default Freesufer on all CentOS6 systems (which includes launchpad, tensor, and the icepuffs) will be updated to a new CentOS6-specific build. The mixed environment this results in can result in confusion for groups with a mix of CentOS versions among their workstations. To avoid this your group should do one of the following: (1) contact the Martinos IT Help Desk to upgrade your old CentOS4 and CentOS5 systems to CentOS6. Sometime in the near future we will drop support all together for the old systems. (2) make a copy of the current CentOS4 release for your study into your group's work area and point your users' environments to use that copy. This is what is recommended for study consistancy anyway and instructions can be found on the wiki at http://surfer.nmr.mgh.harvard.edu/fswiki/MakingPrivateCopiesOfDistributions NOTES: (1) to tell what CentOS version your workstation is running, run on it: cat /etc/redhat-release (2) you are using the default freesurfer release if your PATH has in it directories that start with /usr/local/freesurfer. This is a symlink that currently points to the CentOS4 release on all Linux machines at the center but will change to point at the CentOS6 release on all CentOS6 machines next Monday, the 17th. Feel free to email me with questions. Nick Schmansky ___ All mailing list a...@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all ___ 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] mri_convert mgz to nifti
Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth ___ 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_convert mgz to nifti
mri_convert file.mgz file.nii.gz should do the trick On Tue, 4 Jun 2013, Ray, Siddharth wrote: Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth ___ 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_convert mgz to nifti
The command is 'mri_convert' not 'Mri_convert' -- at least on case sensitive filesystems (like Linux and some-but-not-all Mac OS X). On 6/4/13 10:46 , Ray, Siddharth wrote: Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ 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] Recon-all difficulties off-site
Hi Doug, When I try the command as you suggested: recon-all -all -s unpack3 I get the following error: ERROR: no run data found in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig Do you know why I might be lacking that volume? This was not usually an issue after running the two unpacksdcmdir commands (for MPRAGE and bold runs). Thanks, Adam On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Adam, if the subject folder exists and you pass recon-all a -i flag, then it will exit with error saying that the data exist (otherwise it would overwrite what is there). However, just because the subject folder exists does not mean that there is any data sitting in subject/mri/orig. Then it will tell you that it cannot find any data. Note that when you run recon-all, you need to tell it to do something (eg, add the -all flag to do everything) doug On 06/03/2013 03:21 PM, Nitenson, Adam wrote: Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with. I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i path to structural data -s subject name -force recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use recon-all -s unpack3, I get ERROR: nothing to do I tried a different tactic and used recon-all -s unpack3 -autorecon1 as well as recon-all -autorecon-all -s unpack3 which both created the various folders (bem, label, mri, surf, etc) but failed with ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run of data call it 002.mgz, etc. I have tried these commands in both bash and tcsh shells with the same effect. So the problem, it seems, is that my mri file is blank, and this was not a problem I had running these commands at Martinos. Any idea what the issue might be? Best, Adam Nitenson Neuroscience Graduate Program Laboratory of Affective Neuroscience Brown University ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in
Re: [Freesurfer] mri_glmfit-sim error
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug On 06/04/2013 09:11 AM, Glen Lee wrote: Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote: Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.00 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLowCWPHi NVtxs Annot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] nomotioncor
Hi Bruce, This is certainly something I want to avoid, I guess I won't be using the -nomotioncor flag in any of my studies! I ran recon-all using both only one and two (motion corrected and averaged) source volumes, and the results do seem to suggest that using one vs. two volumes is an empirical issue. In the former case, I tried using the -i switch to point to a specific source volume (as you suggested), but failed to do so for I had already created the subjects' folders. Therefore, in order to use a single source volume, I had to move the remaining ones outside their corresponding mri/orig/ folders. Is there a way around this? I also started using Freeview and I'm finally being able to display the raw volumes cleanly. However, I want to find out why is it that when you change the contrast of your volumes, and avoid saving these changes, every time you reload the volumes they're displayed using the contrast settings you last employed? Why aren't these settings reset to their default values? Thanks! --G if they are named orig/00[012345].mgz then I think they will be averaged but without motion correction, which is almost certainly not what you want On Sun, 2 Jun 2013, obre...@nmr.mgh.harvard.edu wrote: Hi Bruce, Thanks for responding! For the sake of clarification, let's say I have multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i switch in recon-all to point to one of them, exclusively. If I additionally include the -nomotioncor option, will the multiple source volumes be averaged without correcting for motion between them, yielding orig.mgz as output? Best, Gabriel Hi Gabriel if you want to process only one volume, then point recon-all at it with the -i switch. You can also use freeview instead of tkmedit for browsing the volumes - it's much more flexible. The two volumes vs. one is an empirical question. I've found that a single high-quality volume is better than motion-correcting and averaging two, particularly if one of the two is lower quality, but that's an ad hoc assessment on my part and depends a lot on field strength, coil, subject motion, etc cheers Bruce On Sun, 2 Jun 2013, Gabriel Obregon wrote: Hi, Could someone please help me with the following concerns: A. If I have multiple source volumes in mri/orig/ and run recon-all using the -nomotioncor option, how are these inputs processed compared to the case in which motion correction is employed, and what should I expect as my output? B. If I want to process only one of the multiple source volumes, i.e., the best, how should I proceed? C. I've been encountering displaying issues of the raw volumes using tkmedit. What other interfaces are readily available for browsing through the source volumes in order to assess their quality? D. Finally, if in one of my studies I could afford running only two MPRAGE sessions per subject, is motion correction advisable for segmenting the surfaces? Thanks! Gabriel ___ 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.
Re: [Freesurfer] Recon-all difficulties off-site
That dcmunpack command will put the data into a file called unpack3/MPRAGE/002/struct.nii It needs to be put into upack3/mri/orig/002.mgz doug On 06/04/2013 11:22 AM, Nitenson, Adam wrote: Hi Doug, When I try the command as you suggested: recon-all -all -s unpack3 I get the following error: ERROR: no run data found in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig Do you know why I might be lacking that volume? This was not usually an issue after running the two unpacksdcmdir commands (for MPRAGE and bold runs). Thanks, Adam On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Adam, if the subject folder exists and you pass recon-all a -i flag, then it will exit with error saying that the data exist (otherwise it would overwrite what is there). However, just because the subject folder exists does not mean that there is any data sitting in subject/mri/orig. Then it will tell you that it cannot find any data. Note that when you run recon-all, you need to tell it to do something (eg, add the -all flag to do everything) doug On 06/03/2013 03:21 PM, Nitenson, Adam wrote: Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with. I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i path to structural data -s subject name -force recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use recon-all -s unpack3, I get ERROR: nothing to do I tried a different tactic and used recon-all -s unpack3 -autorecon1 as well as recon-all -autorecon-all -s unpack3 which both created the various folders (bem, label, mri, surf, etc) but failed with ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run of data call it 002.mgz, etc. I have tried these commands in both bash and tcsh shells with the same effect. So the problem, it seems, is that my mri file is blank, and this was not a problem I had running these commands at Martinos. Any idea what the issue might be? Best, Adam Nitenson Neuroscience Graduate Program Laboratory of Affective Neuroscience Brown University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
[Freesurfer] v 5.3 pial- FLAIR vs T2
Dear All, Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used as auxiliary for pial definition? Does Freesurfer take care of coregistration between these and the MPRAGE? What would be the command line (Linux Ubuntu) if I want to use SPM generated nifti DICOM concatenations for the T2 or FLAIR, instead of native DICOMs? Thank you, Octavian ___ 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] nomotioncor
isn't that a feature? Freeview saves state to try to preserve the appropriate settings. As for recon-all, yes that is the way it works. If you want to start with a new volume with -i you have to delete the subject dir (or specify a newly named one) cheers Bruce On Tue, 4 Jun 2013, obre...@nmr.mgh.harvard.edu wrote: Hi Bruce, This is certainly something I want to avoid, I guess I won't be using the -nomotioncor flag in any of my studies! I ran recon-all using both only one and two (motion corrected and averaged) source volumes, and the results do seem to suggest that using one vs. two volumes is an empirical issue. In the former case, I tried using the -i switch to point to a specific source volume (as you suggested), but failed to do so for I had already created the subjects' folders. Therefore, in order to use a single source volume, I had to move the remaining ones outside their corresponding mri/orig/ folders. Is there a way around this? I also started using Freeview and I'm finally being able to display the raw volumes cleanly. However, I want to find out why is it that when you change the contrast of your volumes, and avoid saving these changes, every time you reload the volumes they're displayed using the contrast settings you last employed? Why aren't these settings reset to their default values? Thanks! --G if they are named orig/00[012345].mgz then I think they will be averaged but without motion correction, which is almost certainly not what you want On Sun, 2 Jun 2013, obre...@nmr.mgh.harvard.edu wrote: Hi Bruce, Thanks for responding! For the sake of clarification, let's say I have multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i switch in recon-all to point to one of them, exclusively. If I additionally include the -nomotioncor option, will the multiple source volumes be averaged without correcting for motion between them, yielding orig.mgz as output? Best, Gabriel Hi Gabriel if you want to process only one volume, then point recon-all at it with the -i switch. You can also use freeview instead of tkmedit for browsing the volumes - it's much more flexible. The two volumes vs. one is an empirical question. I've found that a single high-quality volume is better than motion-correcting and averaging two, particularly if one of the two is lower quality, but that's an ad hoc assessment on my part and depends a lot on field strength, coil, subject motion, etc cheers Bruce On Sun, 2 Jun 2013, Gabriel Obregon wrote: Hi, Could someone please help me with the following concerns: A. If I have multiple source volumes in mri/orig/ and run recon-all using the -nomotioncor option, how are these inputs processed compared to the case in which motion correction is employed, and what should I expect as my output? B. If I want to process only one of the multiple source volumes, i.e., the best, how should I proceed? C. I've been encountering displaying issues of the raw volumes using tkmedit. What other interfaces are readily available for browsing through the source volumes in order to assess their quality? D. Finally, if in one of my studies I could afford running only two MPRAGE sessions per subject, is motion correction advisable for segmenting the surfaces? Thanks! Gabriel ___ 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] Freesurfer error..recon-all fails
Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani recon-all.log Description: Binary data ___ 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] v 5.3 pial- FLAIR vs T2
Hi Octavian not sure what eT2W FLAIR sense is. The T2_SPACE flair is the only one that we have routinely used that has about 1mm isotropic resolution, and yes we will take care of the registration. Whatever FLAIR you use just point FreeSurfer at it (nifti or dicom) cheers Bruce On Tue, 4 Jun 2013, octavian lie wrote: Dear All, Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used as auxiliary for pial definition? Does Freesurfer take care of coregistration between these and the MPRAGE? What would be the command line (Linux Ubuntu) if I want to use SPM generated nifti DICOM concatenations for the T2 or FLAIR, instead of native DICOMs? Thank you, Octavian ___ 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 error..recon-all fails
Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 error..recon-all fails
yes, there is a file called LICENSE in the freesurfer folder. Should I look for something else? Thanks, Manish From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. LICENSE Description: Binary data ___ 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 error..recon-all fails
Ok I checked the other version of freesurfer and I do have .license file in the freesurfer folder. How can I get this file? Best, Manish From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] recon-all error
Hi Rafa this doesn't look like the whole subject dir, just some files from it (e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our ftp site cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote: Hi Bruce,Thanks for your reply. I have attached the zipped subject dir (please, note that I had to compress it twice for sending problems). Rafa. 2013/6/4 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Rafa that sounds like a bug. Can you gzip and upload the whole subject dir? cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote: Dear freesurfer experts, I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1 #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help will be appreaciated, Many thanks in advance Rafa 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 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 error..recon-all fails
Sorry for the bunch of emails. I registered and got the license file. I have been using this software after a long time and feel silly that this was the thing that was causing trouble. Thank you Doug! Manish From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] mri_nu_correct.mni
Dear FreeSurfers! I want to do bias correction on some T1 and T2 images. I have heard that you can do this by using mri_nu_correct.mni how should I use this command? I could not understand this (I am a beginner in FS) : https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni would it be something like : mri_nu_correct.mni -i path-to-input-file -o path-to-where-output-file-should-be written + filename? Thank you very much! Kind regards, Cris ___ 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] longer run time on 5.3 versus 5.2 ?
Hi Mehul no, that's definitely not expected for it to go from 20 min to almost 5 hours! We'll investigate as that shouldn't be the case. Bruce On Tue, 4 Jun 2013, Mehul Sampat wrote: In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul ___ 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] mris_preproc --qdec-long problem
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the
next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage
--hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45
ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
Hi Chris,
this is a good question for the list (cc'ed), others may or will have the
same problem.
The problem is with your table file, specifically the new line character.
DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.
The problem is that the cat command (at least in linux) does not work on
your file:
cat long.qdec.table.dat is empty
You can convert the \r to \n (linux format):
tr '\r' '\n' long.qdec.table.dat long2.qdec.table.dat
and then should be able to run the preproc command.
People with DOS formats should not run the above tr' command as they will
end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat'
directly (so there is no need)? If anyone on the list knows a good way of
cat and awk a file independently of the new line (and working on all OS),
let me know. This is the command I use:
cat $fsgdf | awk '{if ($1 != fsid substr($1,0,1) != #)
printf(%s.long.%s\n, $1, $2)}'
to generate the subjects id's from the table's first two columns.
Best, Martin
On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
Dr. Reuter,
We corresponded in the past about QDEC, and you gave me great help. The
lab I work for is now moving towards using the Longitudinal Mixed Effects
Model. When I go to run the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target
study_average --hemi lh --meas thickness --out lh.thickness.mgh
I get the error: 'ERROR: no subjects specified.' I am attaching my
long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any
idea of why I am getting this error?
Thanks,
Chris McCarthy
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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.
___
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The information in this e-mail is intended only for the person to whom it is
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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] SPM ROI to Cortical Thickness
Dear FreeSurfer Experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Thank you in advance for your help! Ola Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozra...@childrens.harvard.edumailto:olga.ozra...@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab ___ 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] SPM ROI to Cortical Thickness
Make sure that your SPM volume is registered to the anatomical, then use mri_vol2surf to map the volume to the surface, then mri_segstats to extract the mean of the thickness doug On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: main lab: (617) 355-0400 Dear FreeSurfer Experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Thank you in advance for your help! Ola Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozra...@childrens.harvard.edu mailto:olga.ozra...@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Recon-all difficulties off-site
Hi Doug, The command runs a bit further now but then exits with errors. Unfortunately this time there is no specific stated error. The last few lines of the log are: INFO: extension is mgz # #@# Talairach Tue Jun 4 13:22:08 EDT 2013 /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 EDT 2013 The only other section of the log that seems like it could be related to an error is: Can't locate MNI/Startup.pm in @INC (@INC contains: /gpfs/runtime/opt/perl/5.16.0/lib /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. So, I'm not sure what it's not liking here. Thanks again, Adam On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: That dcmunpack command will put the data into a file called unpack3/MPRAGE/002/struct.nii It needs to be put into upack3/mri/orig/002.mgz doug On 06/04/2013 11:22 AM, Nitenson, Adam wrote: Hi Doug, When I try the command as you suggested: recon-all -all -s unpack3 I get the following error: ERROR: no run data found in /gpfs/data/twhite/anitenso/** FreesurferPractice/unpack3/**mri. Make sure to have a volume called 001.mgz in /gpfs/data/twhite/anitenso/** FreesurferPractice/unpack3/**mri/orig Do you know why I might be lacking that volume? This was not usually an issue after running the two unpacksdcmdir commands (for MPRAGE and bold runs). Thanks, Adam On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Hi Adam, if the subject folder exists and you pass recon-all a -i flag, then it will exit with error saying that the data exist (otherwise it would overwrite what is there). However, just because the subject folder exists does not mean that there is any data sitting in subject/mri/orig. Then it will tell you that it cannot find any data. Note that when you run recon-all, you need to tell it to do something (eg, add the -all flag to do everything) doug On 06/03/2013 03:21 PM, Nitenson, Adam wrote: Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with. I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 -fsfast -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i path to structural data -s subject name -force recon-all -i (path)/FreesurferPractice/**unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use recon-all -s unpack3, I get ERROR: nothing to do I tried a different tactic and used recon-all -s unpack3 -autorecon1 as well as recon-all -autorecon-all -s unpack3 which both created the various folders (bem, label, mri, surf, etc) but failed
Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?
Hi Bruce, Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big change to and are trying to isolate the root cause We are running 75 cases run with 5.3 that have been run with 5.2 before; once they are done, will let you all know if this issue is seen in other cases too. Mehul ps: the cases were run on different machines but the specs of the two machines are quite similar; we are also trying to see if it is hard-ware related.. On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul no, that's definitely not expected for it to go from 20 min to almost 5 hours! We'll investigate as that shouldn't be the case. Bruce On Tue, 4 Jun 2013, Mehul Sampat wrote: In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul 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 information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?
ok, thanks On Tue, 4 Jun 2013, Mehul Sampat wrote: Hi Bruce, Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big change to and are trying to isolate the root cause We are running 75 cases run with 5.3 that have been run with 5.2 before; once they are done, will let you all know if this issue is seen in other cases too. Mehul ps: the cases were run on different machines but the specs of the two machines are quite similar; we are also trying to see if it is hard-ware related.. On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mehul no, that's definitely not expected for it to go from 20 min to almost 5 hours! We'll investigate as that shouldn't be the case. Bruce On Tue, 4 Jun 2013, Mehul Sampat wrote: In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul 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 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] longer run time on 5.3 versus 5.2 ?
I saw this issue too. The total running time went from an average of 16.3h to 20.4h - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Jun 4, 2013 at 2:54 PM, Mehul Sampat mpsam...@gmail.com wrote: Hi Bruce, Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big change to and are trying to isolate the root cause We are running 75 cases run with 5.3 that have been run with 5.2 before; once they are done, will let you all know if this issue is seen in other cases too. Mehul ps: the cases were run on different machines but the specs of the two machines are quite similar; we are also trying to see if it is hard-ware related.. On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul no, that's definitely not expected for it to go from 20 min to almost 5 hours! We'll investigate as that shouldn't be the case. Bruce On Tue, 4 Jun 2013, Mehul Sampat wrote: In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul 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 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 information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
Hi Doug, Yes, we see the same error as in msg28047.html; here is the line from my recon-all.log: mghRead(/mnt/horizon/stage/HLC//004_151_3106223/WBS/Baseline/Freesurfer/mri/ribbon.mgz, -1): could not open file In msg28047.html, Milkos suggested that the issue could be the following line in recon-all set DoSegStats = 1 (in recon-all script in 5.2 this is line 5225; under the case -autorecon2 ) (in recon-all script in 5.3 this is line 5401; under the case -autorecon2 ) I think he is right; first i was confused why this issue was not seen with -autrecon2-cp because there is set DoSegStats = 1 for -autrecon2-cp too; (in recon-all script in 5.3 this is line 5480; under the case -autorecon2-cp) But normally we run -autorecon3 or -all before running -autorecon2-cp; so in this case the ribbon exists and the error does not show up with -autorecon2-cp (if -all or -autorecon3 is run before). Mehul On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The error in msg28047.html is that there was no ribbon.mgz. Is that the error you are receiving? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html On 06/04/2013 01:45 PM, Mehul Sampat wrote: Hi Zeke, Thanks for looking into this; had a quick followup item to report. So for the same subject recon-all -all runs through smoothly; (it was only recon-all -autorecon1 -autorecon2 that generated the error) I had not seen the error before since in the past, my workflow was as follows: 1. run recon-all with -all 2. add control points if required 3. run recon-all with -autorecon2-cp and autorecon3 This ran through without any errors; Now to save some processing time, the modified workflow is: 1. run recon-all with -autorecon1 -autorecon2 2. add control points if required 3. run recon-all with -autorecon2-cp and autorecon3 (It was step 1 in this modified workflow that generated the issue) Mehul ps: the recon-all.log file from the error reported earlier is attached for reference (i sent it to you but forgot to send it to the mailing list earlier) On Thu, May 30, 2013 at 8:31 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Could you provide the recon-all.log file? -Zeke On 05/30/2013 10:24 AM, Gennan Chen wrote: Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will not get created till autorecon3. In V4, that is part of autorecon2 though. Gen On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
Hi Doug, Thanks; Will do so. Also I forgot to mention one thing in the previous email: for case -autorecon3, also there is: set DoSegStats = 1; (in recon-all script in 5.3 this is line 5526) would it help, if set DoSegStats = 1 was used only in -autorecon3 and not in the -autorecon2 or -autorecon2-cp ? or would this break other stuff. Mehul On Tue, Jun 4, 2013 at 11:24 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: this is a bug in mri_segstats. For now, you will need to run recon-all to the end to generate the ribbon.mgz file doug On 06/04/2013 02:12 PM, Mehul Sampat wrote: Hi Doug, Yes, we see the same error as in msg28047.html; here is the line from my recon-all.log: mghRead(/mnt/horizon/stage/**HLC//004_151_3106223/WBS/** Baseline/Freesurfer/mri/**ribbon.mgz, -1): could not open file In msg28047.html, Milkos suggested that the issue could be the following line in recon-all set DoSegStats = 1 (in recon-all script in 5.2 this is line 5225; under the case -autorecon2 ) (in recon-all script in 5.3 this is line 5401; under the case -autorecon2 ) I think he is right; first i was confused why this issue was not seen with -autrecon2-cp because there is set DoSegStats = 1 for -autrecon2-cp too; (in recon-all script in 5.3 this is line 5480; under the case -autorecon2-cp) But normally we run -autorecon3 or -all before running -autorecon2-cp; so in this case the ribbon exists and the error does not show up with -autorecon2-cp (if -all or -autorecon3 is run before). Mehul On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: The error in msg28047.html is that there was no ribbon.mgz. Is that the error you are receiving? http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.** edu/msg28047.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html On 06/04/2013 01:45 PM, Mehul Sampat wrote: Hi Zeke, Thanks for looking into this; had a quick followup item to report. So for the same subject recon-all -all runs through smoothly; (it was only recon-all -autorecon1 -autorecon2 that generated the error) I had not seen the error before since in the past, my workflow was as follows: 1. run recon-all with -all 2. add control points if required 3. run recon-all with -autorecon2-cp and autorecon3 This ran through without any errors; Now to save some processing time, the modified workflow is: 1. run recon-all with -autorecon1 -autorecon2 2. add control points if required 3. run recon-all with -autorecon2-cp and autorecon3 (It was step 1 in this modified workflow that generated the issue) Mehul ps: the recon-all.log file from the error reported earlier is attached for reference (i sent it to you but forgot to send it to the mailing list earlier) On Thu, May 30, 2013 at 8:31 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Could you provide the recon-all.log file? -Zeke On 05/30/2013 10:24 AM, Gennan Chen wrote: Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will not get created till autorecon3. In V4, that is part of autorecon2 though. Gen On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.** edu/msg28047.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it
Re: [Freesurfer] mris_preproc --qdec-long problem
Hi Chris,
still the same (kind of) problem. For some reason you are getting an
empty line in the qdec table so it expands the name to
.long. . Open your long.qdec.table.dat in an editor (e.g. nedit or
gedit), maybe try to copy it into a new editor window, safe it and hope
the editor fixes the problem.
Also try
cat ./qdec/long.qdec.table.dat
to see what it prints, there should be no empty lines.
You can also use hexdump -cb ./qdec/long.qdec.table.dat
to take a look at the files content, there should be single \n at the
end of each line.
Best, Martin
On 06/04/2013 01:41 PM, Christopher McCarthy wrote:
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to
the next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage
--hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45
ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote:
Hi Chris,
this is a good question for the list (cc'ed), others may or will
have the same problem.
The problem is with your table file, specifically the new line
character. DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.
The problem is that the cat command (at least in linux) does not
work on your file:
cat long.qdec.table.dat is empty
You can convert the \r to \n (linux format):
tr '\r' '\n' long.qdec.table.dat long2.qdec.table.dat
and then should be able to run the preproc command.
People with DOS formats should not run the above tr' command as
they will end up with 2 newlines instead of 1. Maybe DOS txt files
work with 'cat' directly (so there is no need)? If anyone on the
list knows a good way of cat and awk a file independently of the
new line (and working on all OS), let me know. This is the command
I use:
cat $fsgdf | awk '{if ($1 != fsid substr($1,0,1) != #)
printf(%s.long.%s\n, $1, $2)}'
to generate the subjects id's from the table's first two columns.
Best, Martin
On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
Dr. Reuter,
We corresponded in the past about QDEC, and you gave me great
help. The lab I work for is now moving towards using the
Longitudinal Mixed Effects Model. When I go to run the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target
study_average --hemi lh --meas thickness --out lh.thickness.mgh
I get the error: 'ERROR: no subjects specified.' I am
attaching my long.qdec.table.dat, which works fine when loaded
by QDEC. Do you have any idea of why I am getting this error?
Thanks,
Chris McCarthy
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652 tel:%2B1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu
reu...@mit.edu mailto:reu...@mit.edu
Web : http://reuter.mit.edu
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.
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
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Re: [Freesurfer] Cortical thickness
Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza desouzajoshu...@gmail.comwrote: Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Joshua, when you add --fwhm 15 to the command line you are instructing mri_glmfit to smooth by 15mm. Is this what you want? Or is the data already smoothed? doug On 6/3/13 12:26 AM, Joshua deSouza wrote: Hi Doug, The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir I am doing a whole hemisphere analysis and am measuring cortical thickness. I do not have my own mask but I have doubts about the mask that has been produced because from previous studies, there has been significant thinning in the area around the hippocampus and parts of it are being left out in the mask, such as the para-hippocampal region. Regards Joshua On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis? doug On 6/2/13 10:29 PM, Joshua deSouza wrote: Hello Doug, Thank you for your quick replies to my queries. Really appreciate it. I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers. I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial) Thank you Joshua On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug On 6/2/13 3:57 AM, Joshua deSouza wrote: Hi Doug, This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly? Thank you Joshua On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug On 05/30/2013 11:21 PM, Joshua deSouza wrote: Hello everyone, Please pardon my rather simple question I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit? And thanks Doug for your help in the other questions that I had prior to this! Thank
