Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

aparc.a2009s+aseg problem
by LAOUCHEDI MAKHLOUF 29 Dec '11

29 Dec '11

hi everyone i run recon-all on 27 subjects using the 5.1 version, and i don't find aparc.a2009s+aseg.mgz neither lh.aparc.a2009s.annot so i can't use the command mri_aparc2aseg ( mri_aparc2aseg --s subject --a2009s). what must i do to have aparc.a2009s+aseg.mgz. thanks

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Corpus callosum aseg division...
by Gonzalo Rojas Costa 29 Dec '11

29 Dec '11

Hi: Any reference about how freesurfer divides the corpus callosum in CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior ?... Sincerely, Gonzalo Rojas Costa

2 1

Setting Up Source File Automatically
by James, Brian 28 Dec '11

28 Dec '11

Hi - I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell type to tcsh. However, when I open my terminal, it doesn't start automatically. I must type 'tcsh' and then it runs. What am I missing? Thanks. Brian James Technical Applications Analyst North Bay Regional Health Centre<http://www.nbrhc.on.ca/> The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur.

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recon-all problem
by LAOUCHEDI MAKHLOUF 28 Dec '11

28 Dec '11

Hi everyone I run freesurfer recon-all command with the flag -all and I have this error ERROR:mpr2mni305 failed, see transforms/talairach_avi.log Some one have any idea? Thanks this is the whole process: Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig/001.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tm mri_convert /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz... mri_add_xform_to_header -c /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/transforms/talairach.xfm /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_ ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux wn033.grid.scg.nuigalway.ie 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 15:20:36 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 6559183 exited with ERRORS at Wed Dec 28 16:21:01 GMT 2011 For more details, see the log file /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa

2 1

FA interpretation from cvs registration for group analysis
by Antonella Kis 28 Dec '11

28 Dec '11

Dear Lilla, I will appreciate a lot if you can help me understand what is the meaning of the results after running after running mri_cvs_register and the GLM group analysis. More exactly, I followed all the instructions from the webpage: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion and I wonder if based on the cluster's colours I can say something about my FA values in one group related to the other one. More exactly I am looking to understand if I have an increase in the FA value for the controls versus patients or the FA in patients is larger than in the control group. My contrast matrix is C = [+1.00000 -1.00000 ] and I have 30 controls and 32 patients. What is the age range for the cvs_avg35 space? I wonder if is the best space to register my subjects if they are children with age between 6-14. Thank you very much! Antonella

2 6

Question after preprocessing in FreeSurfer.
by Long 27 Dec '11

27 Dec '11

Dear all, Hi, I am a beginner of FreeSurfer. Recently I have run recon-all and preproc-sess on my MRI and fMRI images. Next I'd like to convert surface images to AFNI-SUMA and convert fMRI images to volume space. I found that the T1 image and its surface maps were not normalized and the fMRI images were normalized into MNI305 in surface space. So my question is, how to normalize the T1 surface maps by using talairach.xfm, so I can view the normalized surface maps in SUMA, and how to convert surface space fMRI images (i.e., fmcpr.up.sm5.fsaverage.lh.nii.gz) to the volume space? Thank you in advance! Best, Xiangyu

1 0

freeview auditory cortex etc.
by Klein, Holger 25 Dec '11

25 Dec '11

Dear freesurfers, 1) I have a little question concerning Freeview: As attachment there are 3 screenshots, which show a label of the 2009 atlas (Primary auditory cortex). I used brain.mgz as "input" volume and chose the label in the ROI tab in freeview - but the screenshots look like as if there is a vast part of the labeled cortex not colored. I'm wondering why the other cortical voxels - which definitely belong to Heschl-Gyrus (A1) - are not marked? I thought that a label marks all the pixels/voxels (also in 2D view) between the white matter surface and the pial surface that belong to the chosen cortical structure. Am I mistaken by interpreting the meaning of a label in this way? 2) Actually I got stuck when trying to find a good 3D-view of Heschl'Gyrus (lh.G_temp_sup-G_T_transv.label) cause it is hidden in the deep Sylvian fissure. Is there a possibility to get a better view on this label (e.g. transparent view of the surrounding brain structures)? I attached another screenshot (Schneider, Cortex) which was taken from a colleague of mine working with brainvoyager - is it possible to create something like this in freesurfer/freeview? Looking forward to answers, thanks a lot... Holger

1 0

freeview label
by Klein, Holger 25 Dec '11

25 Dec '11

Dear Freesurfers, Merry Christmas to all of you!!! I have a little problem with freeview: As attachment there are three screenshots, which show two labels of the 2009 atlas (Primary auditory cortex und primary visual cortex). I used brain.mgz as "input" volume and chose the labels in the ROI tab in freeview - but the screenshots look like as if there is a vast part of the labeled cortex not colored? What could be the reason for this? Thx a lot & best wishes for 2012, Holger

2 1

Talairach transform issue; V 5.0
by Andy Mayer 24 Dec '11

24 Dec '11

Hello Freesurfer Experts- We recently reran several subjects from scratch through the stable Freesurfer 5.0 pipeline who had previously been processed with the stable 4.5 pipeline. We used tkregister2 for QA of the 5.0 data and noticed that the talairach transform was off (misaligned) for the first 5 subjects we examined. All subjects passed the auto Talairach check, and their 4.5 data was not misaligned. Applying the talairach.xfm matrix from the 4.5 pipeline corrected the problem. Looking at the recon-all.cmd files from the different versions, it looks like the only difference for the tailairach_avi step was that the 4.5 version called for nu.mgz whereas the 5.0 version called for orig.mgz. I reran a couple of 5.0 subjects using talairach_avi --i nu.mgz –xfm transforms/talairach.auto.xfm Doing this fixed the transform and subsequent alignment problems (copied above to talairach.xfm and re-ran tkregister2). I have read on the list that the talairach.xfm is not used in the majority of data streams (although table indicates otherwise). Our plans were to use the data for both cortical thickness analyses as well as MEG analyses (source mapping). I would appreciate it if someone could tell me: 1) The best way to rerun the current data that has been run through 5.0. We have already run about 50 of 100 subjects through 5.0. 2) The best way to fix our recon-all program for 5.0 so that the correct transform is generated for new subjects. 3) In addition, we also observed the following error in the log file and could not find any information on what it may mean (all checked subjects had error) *********************************************** Computing MAP estimate using 3481 samples... *********************************************** IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... Thanks for your time! Andrew

2 2

Noise filtering before recon-all
by Courtney Haswell 23 Dec '11

23 Dec '11

We have some T1 images that are kind of noisy that were acquired several years ago. We applied a noise-reduction filter (FSL's SUSAN) to the T1 images before beginning the recon-all segmentation process. Is there any reason not to do this type of smoothing before recon-all, or is there any option in the recon-all pipeline to filter noise? Is it recommended to apply a filter before recon-all in this case? Thanks, Courtney

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