[Freesurfer] Load Brodmann surface area into inflated surface
Hi all, I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here): I'm using version 5.0.0. I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar? Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks in advance, Andreia ___ 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] Help Error running recon-all-s during installation test
Dear all, I am new freesurfer user (version 5.0.0 installed to windows using virtual machine), during the installation i was trying to test the installation, following the recommended steps. The recon-all -s terminated with errors, andi can't find the bug. I send you the command line and the report including the error message to help you. -- FREESURFER_HOME /home/virtualuser/freesurfer SUBJECTS_DIR /home/virtualuser/freesurfer/subjects -- FreeSurfer:~ recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz... /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz... # #@# MotionCor Mon Apr 23 04:55:18 EDT 2012 Found 2 runs /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /home/virtualuser/freesurfer/subjects/ernie mri_robust_template --mov /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 --template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as movable/source volume. --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'... reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] = TP 2 to TP 1 == Register TP 2 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz ) to TP 1 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1.32812)mm and dim (256, 256, 128) Dst: (1, 1, 1.32812)mm and dim (256, 256, 128) Asserting both images: 1mm isotropic and (256, 256, 170) voxels Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation Original : (1, 1, 1.32812) mm size and (256, 256, 128)
Re: [Freesurfer] trakula segmentation fault
Hello Anastasia, It fixed the bug. Thank you so much! Now Im running trac-all -bedp -c But it's been running for already 3 days, and it just printed that: trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer INFO: Diffusion root is /media/vivi/images/freesurfer Actual FREESURFER_HOME /media/vivi/code/freesurfer ln -sf /media/vivi/images/freesurfer/00112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /media/vivi/images/freesurfer/00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage Is it normal? Thanks for your help! (let me know if I should create another thread) Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI template brain, and our atlas was built using the 1mm one. From your dmrirc file: # MNI template (the only option for inter-subject registration in this version) # Default: $FSLDIR/data/standard/MNI152_**T1_1mm_brain.nii.gz # #set mnitemp = /path/to/mni_template.nii.gz set mnitemp = /usr/share/fsl/4.1/data/**standard/MNI152_T1_2mm_brain.** nii.gz Can you please try changing the above from 2mm to 1mm and see if it works? If so, I'll make sure this is handled more elegantly in the next version. Hope this helps, a.y On Fri, 6 Apr 2012, Viviana Siless wrote: Hi Anastasia, Here is the data: https://transfert.inria.fr/**fichiers/** 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gzhttps://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything wrong! Thank you! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Viviana - If you upload this data set I'm happy to look at it. Also, I strongly recommend getting the updated version of trac-all from the wiki (I'm guessing from the log file that you're probably not using that?) See 2012/01/09 update here: http://surfer.nmr.mgh.**harvard.edu/fswiki/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/Tracula Thanks, a.y On Wed, 4 Apr 2012, Viviana Siless wrote: Hello, I'm trying to run trac-all prec and I'm getting a segmentation fault error. Loading streamlines from /media/vivi/code/freesurfer/** trctrain/trc032/dlabel/mni/lh.**cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/** trctrain/trc033/dlabel/mni/lh.**cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/** trctrain/trc033/dlabel/mni/lh.**cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/** trctrain/trc033/dlabel/mni/lh.**cst_AS.flt.trk INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012 - When I look at the trak-all.error I see this error: -- SUBJECT 00112288Proc DATE Wed Apr 4 18:24:21 CEST 2012 USER vivi HOST vivi-ThinkStation-C20X PROCESSOR x86_64 OS Linux Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /media/vivi/code/freesurfer/**bin/trac-preproc PWD /media/vivi/code/freesurfer CMD /media/vivi/code/freesurfer/**bin/dmri_train --outdir /media/vivi/images/freesurfer/**00112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt
Re: [Freesurfer] improving automated cerebellar parcellation
Hi Anthony,
in matlab it would be something like:
vaseg = load_mgh('aseg.mgz') ;
[vmanual,M,mr] = load_mgh('manual_seg.mgz') ;
ind = find(vmanual 0) ;
vaseg(ind) = vmanual(ind) ;
save_mgh(vaseg, 'manual_seg.with_aseg.mgz', M, mr) ;
cheers
Bruce
On Sun, 22 Apr 2012, Anthony Dick
wrote:
Hi Bruce,
Can you point me somewhere in the right direction? Is there some example I
could start with? I don't use Matlab, although it seems similar to R so I
should be okay with learning the syntax, but I just need a place to start.
Anthony
On 4/20/12 4:02 PM, Bruce Fischl wrote:
probably in matlab
On Fri, 20 Apr 2012, Anthony Dick wrote:
Thanks Bruce. What's the easiest way to paste those labels. Manually
through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
HI Anthony
I would make sure to include an entire brain labeling in the training
set. You can do this by pasting your manual labels into our aseg of the
subjects in question.
cheers
Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20
brains manually segmented by Jörn Diedrichsen, which he was kind enough
to share (note these also formed the basis for his 2009 paper in
Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As
you can see from the attached image, it is not ready for prime-time. On
the left is the brain of subject 1, manually segmented. On the right is
the brain of the same subject with the automated sementation, based on
the developed atlas.
My question is, how can I improve it? I realize this is an open question
and potentially difficult to answer without some probing, but this is a
resource I think a lot of users would like to have access to, so perhaps
it is worth the effort.
Anthony
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] Help Error running recon-all-s during installation test
Hi Statos how much RAM do you have in your machine? It looks like not enough. cheers Bruce On Mon, 23 Apr 2012, Eustratios Karavasilis wrote: Dear all, I am new freesurfer user (version 5.0.0 installed to windows using virtual machine), during the installation i was trying to test the installation, following the recommended steps. The recon-all -s terminated with errors, andi can't find the bug. I send you the command line and the report including the error message to help you. -- FREESURFER_HOME /home/virtualuser/freesurfer SUBJECTS_DIR /home/virtualuser/freesurfer/subjects -- FreeSurfer:~ recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz... /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz... # #@# MotionCor Mon Apr 23 04:55:18 EDT 2012 Found 2 runs /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /home/virtualuser/freesurfer/subjects/ernie mri_robust_template --mov /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 --template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as movable/source volume. --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'... reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] = TP 2 to TP 1 == Register TP 2 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz ) to TP 1 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1.32812)mm and dim (256, 256, 128) Dst: (1, 1, 1.32812)mm and dim (256, 256, 128) Asserting both images: 1mm isotropic and (256, 256, 170) voxels Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256,
Re: [Freesurfer] Load Brodmann surface area into inflated surface
Hi Andreia sorry, I don't understand. What do you mean when you say you want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects. Do you mean just to show what portion of the surface is in each of 3 Brodmann areas? That you would do by loading the relevant labels, although you will probably want to threshold them differently (e.g. V1 you could threshold at .9 which is 90% and it would have about the surface area of an individual, while MT would need to be closer to .4 or .5). Or do you actually mean the volume of gray matter within each BA? If the latter, it's just 3 numbers/subject, so I would think you would want a scatter plot or something, not a map on the surface. cheers Bruce On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: Hi all, I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here): I'm using version 5.0.0. I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar? Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks in advance, Andreia ___ 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] surface does not match
Hi Ruthger that means that the subject was partially reprocessed but not completed. You can finish it with: recon-all -s subject -sd subjects dir -make all cheers Bruce On Thu, 19 Apr 2012, Righart, Ruthger Dr. wrote: Dear Freesurfers, I analyzed a dataset with FS 5.1 but upon loading the data in tksurfer I get the following error: mrisReadTriangleFile(/.../surf/lh.sphere.reg): surface doesn't match /.../surf/lh.inflated The same error occurs when I run mris_preproc as a step before GLM analyses (mri_glmfit). A similar problem was described in the mailing list and offered the possibility to resolve this with the following command: recon-all -s subjid -make all This command only runs at the moment for a few of my subjects (I am at the moment waiting for the results of these analyses). For the majority of my subjects having the same error in mrisReadTriangleFile this command does not run. For those, it seems that the command -make all is not recognized. Does anyone know why it does not run or is there an alternative solution in FS 5.1. for this problem? Thank you very much in advance for your help! Ruthger Righart ___ 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] prefrontal cortex values
for all of prefrontal you mean? No, but it would be easy enough to draw a label on fsaverage for prefrontal, then map it to every one of your individual subjects using mri_label2label. cheers Bruce On Thu, 19 Apr 2012, Ahmed, F, Me fah...@sun.ac.za wrote: Hello FS experts, A quick question for you all. Does the FS stream produce any values for the Prefrontal Cortex specifically? Thanks, Fatima E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this 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] Neuroscience project, hippocampus segmentation
Hi, I'm currently doing a project for my neuroscience course. I've decided to compare automatic segmentation methods (comparing hippocampus volumes) (using Freesurfer and FIRST). My question is, whether there is a set of commands in Freesurfer which will enable me to segment only hippocampus. I'm only intrested in volumes, nothing else. I've noticed that recon-all takes a lot of time and been wandering if there is a faster way. Pawel ___ 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] Neuroscience project, hippocampus segmentation
Hi Pawel no, sorry, you need to segment everything to get hippocampal volumes. You can stop after autorecon2 and not run 3, which will save you a bit of time, but you are probably better off just running them all normally. cheers Bruce On Mon, 23 Apr 2012, Pawe? Dembi?ski wrote: Hi, I'm currently doing a project for my neuroscience course. I've decided to compare automatic segmentation methods (comparing hippocampus volumes) (using Freesurfer and FIRST). My question is, whether there is a set of commands in Freesurfer which will enable me to segment only hippocampus. I'm only intrested in volumes, nothing else. I've noticed that recon-all takes a lot of time and been wandering if there is a faster way. Pawel ___ 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] Load Brodmann surface area into inflated surface
(forgot to do answer all, here it goes for the list too) Citando _andre...@sapo.pt: Hi Bruce, The ideia is to show one control subject vs. one patient inflated surface with BA surface (not volume, sorry) to show the difference (reduced surface area in one patient). Loading the relevant labels worked (I have the statistics shown in bar graphs, the images are only for visualizing the difference between controls and patients). When I threshold the labels in the subject's inflated surface they shrink a lot, is this supposed to happen? The BA are V1, V2 and MT. What is the thresghold for V2? And is it correct to load ?h.sulc in a gray scale to have the usual cortex representation, or I should do it other way? And getting back to my previous email: Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks, Andreia Citando Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia sorry, I don't understand. What do you mean when you say you want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects. Do you mean just to show what portion of the surface is in each of 3 Brodmann areas? That you would do by loading the relevant labels, although you will probably want to threshold them differently (e.g. V1 you could threshold at .9 which is 90% and it would have about the surface area of an individual, while MT would need to be closer to .4 or .5). Or do you actually mean the volume of gray matter within each BA? If the latter, it's just 3 numbers/subject, so I would think you would want a scatter plot or something, not a map on the surface. cheers Bruce On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: Hi all, I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here): I'm using version 5.0.0. I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar? Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks in advance, Andreia ___ 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
Re: [Freesurfer] bbregister for fmri FEAT data
Hi Erlend, while the images in the tkregister2 pics are oriented correctly the registration is way off. What images are you loading into fslview? You'll need to convert the orig.mgz into nii and load that to check the registration. doug On 04/22/2012 04:16 AM, Erlend Hodneland wrote: Hi again, the registration looks fine in tkregister2, but is apparently wrong in fslview (and also mricron). See the attached files (as link from http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing screenshots of fslview and tkregister2. How can this be explained, and how can we visualize the correct orientation in fslview? What does this misalignment influence any further processing with fnirt and concatenation of the affine transformation fields? This is our command we run for bbregister: bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat --init-fsl --t2 --o test.nii.gz where vol0001 is the first volume in the fmri sequence and is flipped to align with LAS (as the highres). Thank you for your kind help, Erlend Hodneland ean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug On 04/13/2012 03:31 AM, Erlend Hodneland wrote: Hi, we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT. However, the orientation of the registered image is flipped around and is incorrect after applying bbregister. We have tried: 1) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat myfeatdirectory 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii 5) reorienting to match the highres: fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct orientation) followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii with the output being flipped in wrong orientation for all options. We would greatly appreciate if you have any suggestions for how to overcome this problem! Cheers/Sincerly/All best Erlend Hodneland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Load Brodmann surface area into inflated surface
Hi Andreia, yes, they will always shrink since the label contains every point that could possibly be in the BA, no matter how unlikely. I'll try to find time to automatically threshold the BAs so that they have the average area of the individual examples, but for now V2 is probably around .7 and MT around .4 I think. And yes, I would use ?h.sulc as the background gray scale. The volume of the BAs would be computed using both surfaces, but the surface area can be from either one. I think we use the white by default, but you can use label_area to measure on whatever surface you want. cheers Bruce On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: (forgot to do answer all, here it goes for the list too) Citando _andre...@sapo.pt: Hi Bruce, The ideia is to show one control subject vs. one patient inflated surface with BA surface (not volume, sorry) to show the difference (reduced surface area in one patient). Loading the relevant labels worked (I have the statistics shown in bar graphs, the images are only for visualizing the difference between controls and patients). When I threshold the labels in the subject's inflated surface they shrink a lot, is this supposed to happen? The BA are V1, V2 and MT. What is the thresghold for V2? And is it correct to load ?h.sulc in a gray scale to have the usual cortex representation, or I should do it other way? And getting back to my previous email: Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks, Andreia Citando Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia sorry, I don't understand. What do you mean when you say you want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects. Do you mean just to show what portion of the surface is in each of 3 Brodmann areas? That you would do by loading the relevant labels, although you will probably want to threshold them differently (e.g. V1 you could threshold at .9 which is 90% and it would have about the surface area of an individual, while MT would need to be closer to .4 or .5). Or do you actually mean the volume of gray matter within each BA? If the latter, it's just 3 numbers/subject, so I would think you would want a scatter plot or something, not a map on the surface. cheers Bruce On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: Hi all, I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here): I'm using version 5.0.0. I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar? Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks in advance, Andreia ___ 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
Re: [Freesurfer] labelling of cluster regions
Hi Koushik, it just uses the label of the maximum. doug On 04/19/2012 05:30 PM, Govindarajan, Koushik Athreya wrote: Hi, I have a question regarding how the clusters are labeled after the results of a Monte-Carlo Simulation. Similar regions from 2 different patient populations seem to be labeled differently. On one of my results, the cluster has been labeled as in the precentral region and a similar region on another population seems to be labeled as superior frontal region. Is the labeling based on which region the majority of significant vertices fall under? In that case, would a cluster that kind of falls over 2 regions of the brain be labeled as the one with more vertices? Thanks for all the help Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
Hi Xiangyu, just add --identity fsaverage to the surf2vol command line doug On 04/19/2012 05:57 PM, Long wrote: Hi all, I had a question when convert a surface to volume space. First, I converted a volume nifti data to fsaverage: mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat --out data.lh.mgh Then, I want to convert the data.lh.mgh to volume space, I tried mri_surf2vol, however, it needs register.dat. As I understood, the data.lh.mgh was already registered to fsaverage surface, so how can I get the required register.dat file? Thank you for your attention. Best, Xiangyu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM modification
Hi Doug,I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file.I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution?Bests,GabrielEl 17/04/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linuxThe only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot.dougOn 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM modification
Hi Gabriel, I'll need to wait for Nick or Krish to respond to this one. N/K: I'm trying to give Gabriel a new version of mri_segstats that I compiled on Linux tanha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux doug On 04/23/2012 10:35 AM, Gabriel Gonzalez Escamilla wrote: Hi Doug, I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message: mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats). Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file. I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution? Bests, Gabriel El 17/04/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux The only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot. doug On 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM modification
Gabriel: try running ldd on the mri_segstats and see what libraries it is trying to find and whether you have them all. cheers Bruce On Mon, 23 Apr 2012, Douglas N Greve wrote: Hi Gabriel, I'll need to wait for Nick or Krish to respond to this one. N/K: I'm trying to give Gabriel a new version of mri_segstats that I compiled on Linux tanha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux doug On 04/23/2012 10:35 AM, Gabriel Gonzalez Escamilla wrote: Hi Doug, I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message: mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats). Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file. I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution? Bests, Gabriel El 17/04/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux The only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot. doug On 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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_expand not working since upgrading to v.5.1.0
I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP). I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 Hi Andrew, I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works. cheers Bruce p.s. do you look at the surfaces via: freeview -f lh.white lh.white.expanded On Fri, 20 Apr 2012, Andrew C Yourich wrote: Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0
can you try it on a linux machine? On Mon, 23 Apr 2012, Andrew C Yourich wrote: I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP). I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 Hi Andrew, I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works. cheers Bruce p.s. do you look at the surfaces via: freeview -f lh.white lh.white.expanded On Fri, 20 Apr 2012, Andrew C Yourich wrote: Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0
I personally do not have access to a Linux machine, but I do know someone in our department that does run freesurfer on one. I had e-mailed him on Friday to see if he encountered this issue as well, so let me follow up with him and see if he is able to check mris_expand results on his computer. - Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, April 23, 2012 9:44 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu; Robert C Knowlton; gramf...@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 can you try it on a linux machine? On Mon, 23 Apr 2012, Andrew C Yourich wrote: I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP). I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 Hi Andrew, I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works. cheers Bruce p.s. do you look at the surfaces via: freeview -f lh.white lh.white.expanded On Fri, 20 Apr 2012, Andrew C Yourich wrote: Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew 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
[Freesurfer] your insight: parameter definition and --tnullmin necessary?
Dear Freesurfer list, I am using optseq2 for the first time and wanted to check with you whether my protocol makes sense, many thanks in advance for your insight. 1) I start by choosing the maximum scan duration equalling ~30 min: 2) set the psd window so it can capture the entire waveform of a 4 second event 3) select equal amounts of trials for each of the 4 event types, I played around with it and 80 trials give me the greatest efficiency (2.72) and variance reduction factor average (54.37). Are these values acceptable? They are the best I could get tweaking the number of trials. The command is here: ./optseq2 --ntp 440 --tr 4 --psdwin 0 20 \ --ev evt1 4 80 \ --ev evt2 4 80 \ --ev evt3 4 80 \ --ev evt4 4 80 \ --nkeep 3 \ --o gfatrial \ --focb 10 \ --nsearch 1 A sample trial list is here: 0.24.000 1. evt2 4.44.000 1. evt4 8.04.000 1. NULL 12.34.000 1. evt3 16.34.000 1. evt3 20.24.000 1. evt2 … The other question I had concerns the position of null trials. Many trials are not separated by a NULL event, however studies of rapid event-related designs to report a minimum ITI, in this case the minimum seems to be 0? To assess the effect of forcing a minimum ITI on the sequence, I have run the search defining the --tnullmin to 4 sec (equal to 1 TR) however efficiency and VRFAvg drop to .79 and 16.07, obviously due to trade of between ntp and ntrials (ntp=440, ntrials=62). Are NULL trials between each event required at all if a standard FIR is used for the analysis? My aim is to first apply a univariate BOLD-analysis and subsequently a multivariate analysis to the dataset. Thanks for clarifying. Betina ___ 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] How to convert a surface to volume space after using mris_preproc?
Hi Douglas, I tried to do spatial normalization for volume data, all steps are following: 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01 --init-fsl --reg bb_register.dat I checked the result by tkregister2, it looked good. 2) mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr bb_register.dat --projfrac 0.5 --out lh.zmap.mgh 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity fsaverage --outvol subj01_001.nii.gz --projfrac 0.5 --fillribbon --template wfrest_res_co_001.hdr However, the output file subj01_001.nii.gz showed wrong orientation when viewing in MRIcron, the image looked rotated. Could you please help with it? Best, Xiangyu On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Xiangyu, just add --identity fsaverage to the surf2vol command line doug On 04/19/2012 05:57 PM, Long wrote: Hi all, I had a question when convert a surface to volume space. First, I converted a volume nifti data to fsaverage: mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat --out data.lh.mgh Then, I want to convert the data.lh.mgh to volume space, I tried mri_surf2vol, however, it needs register.dat. As I understood, the data.lh.mgh was already registered to fsaverage surface, so how can I get the required register.dat file? Thank you for your attention. Best, Xiangyu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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_cvs_register error in step 2
hi Lilla, I ended up with the same error... so I'm not sure what else to try. Do you have an ideas for troubleshooting? I've also attached the latest log file, although it's probably very similar to the first one. thanks, jackie On Fri, Apr 20, 2012 at 6:10 PM, Jackie Leung jackie.le...@alumni.utoronto.ca wrote: The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview. Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register --mov sub26 --template sub47 --outdir CVS_test_26to47_1 --step2 --nocleanup The same error pops up. very puzzling. i will rerun everything overnight to see if i get the same problem. thanks, jackie On Fri, Apr 20, 2012 at 3:56 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then they will be regenerated. --Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: ok... please see attached. note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories. thanks, jackie On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, Could you attach the log file? Thanks, Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.**resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.**white I've checked the directory and the file definitely exists. It seems to be popping up in step 2 of the script, where it calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be. Any help will be greatly appreciated! thanks, jackie 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. -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 sub26_to_sub47.mri_cvs_register.1204201815.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] mri_cvs_register error in step 2
Hi Jackie, Sorry that the error is still there. Are you sure that the attached log file is for the below command? I am asking as the log file indicates that spherical registration is done and that should not happen in Step2. Also, could you tell me which version of the FS distribution you are using? This might be somethig that got fixed in the past. Lilla On Mon, 23 Apr 2012, Jackie Leung wrote: hi Lilla, I ended up with the same error... so I'm not sure what else to try. Do you have an ideas for troubleshooting? I've also attached the latest log file, although it's probably very similar to the first one. thanks, jackie On Fri, Apr 20, 2012 at 6:10 PM, Jackie Leung jackie.le...@alumni.utoronto.ca wrote: The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview. Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register --mov sub26 --template sub47 --outdir CVS_test_26to47_1 --step2 --nocleanup The same error pops up. very puzzling. i will rerun everything overnight to see if i get the same problem. thanks, jackie On Fri, Apr 20, 2012 at 3:56 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then they will be regenerated. --Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: ok... please see attached. note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories. thanks, jackie On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, Could you attach the log file? Thanks, Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.white I've checked the directory and the file definitely exists. It seems to be popping up in step 2 of the script, where it calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be. Any help will be greatly appreciated! thanks, jackie 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. -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 ___ 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] Error: matrix is rank-deficient by 2
Hello, We are getting the following error while processing T1 data acquired on Philips. The image data looks ok. We have three scans with similar error. Does anyone have suggestions as to what could be wrong? Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Linux node159 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x 86_64 GNU/Linux recon-all -s 0180634_v00_mr exited with ERRORS at Mon Apr 2 12:25:57 CDT 2012 ___ 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] your insight: parameter definition and --tnullmin necessary?
Hi Betina, see answers below doug On 04/23/2012 12:04 PM, Betina Ip wrote: Dear Freesurfer list, I am using optseq2 for the first time and wanted to check with you whether my protocol makes sense, many thanks in advance for your insight. 1) I start by choosing the maximum scan duration equalling ~30 min: You might want to break this up into shorter chunks. It's totally up to you, you just don't need to have everything in a single run. 2) set the psd window so it can capture the entire waveform of a 4 second event 3) select equal amounts of trials for each of the 4 event types, I played around with it and 80 trials give me the greatest efficiency (2.72) and variance reduction factor average (54.37). Are these values acceptable? They are the best I could get tweaking the number of trials. You can't tell whether a VRF of 54 is good enough. You are asking a question about the power of your experiment, which optseq can't answer. If you don't have an effect, then no number of trials or efficiency will be good enough. Having said that, I usually shoot for a VRF of between 20 and 40, but that's just a rule of thumb. The command is here: ./optseq2 --ntp 440 --tr 4 --psdwin 0 20 \ --ev evt1 4 80 \ --ev evt2 4 80 \ --ev evt3 4 80 \ --ev evt4 4 80 \ --nkeep 3 \ --o gfatrial \ --focb 10 \ --nsearch 1 A sample trial list is here: 0.24.000 1. evt2 4.44.000 1. evt4 8.04.000 1. NULL 12.34.000 1. evt3 16.34.000 1. evt3 20.24.000 1. evt2 … The other question I had concerns the position of null trials. Many trials are not separated by a NULL event, however studies of rapid event-related designs to report a minimum ITI, in this case the minimum seems to be 0? To assess the effect of forcing a minimum ITI on the sequence, I have run the search defining the --tnullmin to 4 sec (equal to 1 TR) however efficiency and VRFAvg drop to .79 and 16.07, obviously due to trade of between ntp and ntrials (ntp=440, ntrials=62). Are NULL trials between each event required at all if a standard FIR is used for the analysis? My aim is to first apply a univariate BOLD-analysis and subsequently a multivariate analysis to the dataset. Thanks for clarifying. They are not strictly necessary, however, they may be helpful. If you really don't want them as part of your design (eg, it would interfere with the psychology), then don't use them but make sure to optimize the FOCB more (I usually use 100 regardless). The disadvantage of not having the nulls is that there will probably be some non-linearity in that the second of two closely spaced trials will have a lower amplitude than if it occurred in isolation. This will hurt your power and might cause a false difference between conditions if they are not well counter-balanced. doug Betina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error: matrix is rank-deficient by 2
Is this one of the new dicom format files? The new ones have a single dicom file with all the pixel data in it (and we can't read them yet). doug On 04/23/2012 03:22 PM, Mohana Ramaratnam wrote: Hello, We are getting the following error while processing T1 data acquired on Philips. The image data looks ok. We have three scans with similar error. Does anyone have suggestions as to what could be wrong? Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficient by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Linux node159 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x 86_64 GNU/Linux recon-all -s 0180634_v00_mr exited with ERRORS at Mon Apr 2 12:25:57 CDT 2012 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Normalization Questions
Hello, Thank you Michael for your input. My feeling was that surface area would scale with ICV. In any case, is there any recommendation on how to normalize the Jacobian? My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian? My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization? I hope that makes sense. Any feedback would be very greatly helpful! Mahalo, Jeff Hi Jeff, I'm confused here. ICV and surface area are two very different things. cheers, -MH On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino jsadino.que...@gmail.comwrote: Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this? Thank you, Jeff On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms mha...@conte.wustl.eduwrote: Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby address whether any regional thickness differences were in excess of global cortical thickness differences between groups -- see references [1,4] in our Reply. cheers, -MH Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mha...@conte.wustl.eduwrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html ). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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 ___ 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] Freeview Edit Capability
Hi Freesurfers, I just want to check my observation that Freeview can not currently be used for editing the WM.mgz or the brainmask.mgz (for minor skull strip errors) as is done in TKmedit (cf., Edit Tutorial). Is that correct? I can’t find any documentation on this, and whilst I would assume it to be a straightforward thing if possible, I can’t work out how I could configure Freeview voxel edit tools to do this. I assume that the only edits currently possible in freeview are label/ROI edits and control point definition. If this is correct, will the other edits become possible in later versions of Freeview? – this would be great given the ability to load multiple volumes…for example it is nice to view the brainmask.mgz over the T1.mgz with the latter’s opacity turned down in order to quickly detect minor skull strip errors. It would be then nice to delete (or clone-in) voxels on this set of images (like TKmedit). Thanks for your help R ___ 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] About the GroupAnalysis
Hi All, When we do the GroupAnalysis,there is a vector(such as: 0 0 0.5 0.5).And I just want to know how this vector involve in calculating? ___ 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] Edit Capability of Freeview
So shorlty after I sent that email I figured out how to do a little of what I spoke about... a) White matter (WM.mgz) edits - joining WM fingers in the WM.mgz or filling holes, etc..Should New WM voxels in WM.mgz should be = 255 (brush value)?? b) I can delete skull/dura..should I be replacing values in dura/skull voxels with 1 or 0 or what? Can I do cloning like in TKmedit such that I could replace small bits of skull-stripped cerebellum in the brainmask.mgz by cloning from the T1.mgz? In the voxel edits toolbar, what is the reference option for? I was hoping that it would be for cloning, but apparently not R ___ 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] About the GroupAnalysis
It's hard to say without more information, but that looks like a contrast vector which is used to test a hypothesis. On 4/23/12 9:00 PM, bowan...@mail.ustc.edu.cn wrote: Hi All, When we do the GroupAnalysis,there is a vector(such as: 0 0 0.5 0.5).And I just want to know how this vector involve in calculating? ___ 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] Cortical Normalization Questions
Why do you want the jacobian? The surface area is a more interpretable measure. If you use surface area, make sure you get the patch for mris_preproc. doug On 4/23/12 8:07 PM, Jeff Sadino wrote: Hello, Thank you Michael for your input. My feeling was that surface area would scale with ICV. In any case, is there any recommendation on how to normalize the Jacobian? My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian? My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization? I hope that makes sense. Any feedback would be very greatly helpful! Mahalo, Jeff Hi Jeff, I'm confused here. ICV and surface area are two very different things. cheers, -MH On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino jsadino.que...@gmail.com mailto:jsadino.que...@gmail.com wrote: Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this? Thank you, Jeff On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms mha...@conte.wustl.edu mailto:mha...@conte.wustl.edu wrote: Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby address whether any regional thickness differences were in excess of global cortical thickness differences between groups -- see references [1,4] in our Reply. cheers, -MH Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mha...@conte.wustl.edu mailto:mha...@conte.wustl.eduwrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ Freesurfer mailing list 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
