Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

lGI value aberrantly too high but no topological defect
by Christian Scheel 10 Feb '09

10 Feb '09

Dear Marie, dear all, just to let you know: I have successfully overcome the problem by relaunching recon-all -hemi ?h -autorecon2 -autorecon3 for the brain in question. After the relaunch the lGI calculation worked perfectly and finished without errors. Best regards, Christian Scheel ### Dear Christian, I am aware that the lGI may occasionnally exit with the error you mentionned in some rare cases of pial surfaces with normal euler neumbers. I am working on debugging it. In the mean time, if this is only for one subject, is it possible for you to recreate the surfaces just for the hemisphere where you have this problem (i.e. relaunching recon-all -hemi ?h -autorecon2 and -autorecon3)? This would probably be the easiest way to overcome the aberrantly high lGI issue, as it will change very slightly the position and the total number of vertices of the white and pial surfaces, which will normally solve the problem. However, that implies that you would have to redo any statistical analyses that you may have already done on cortical thickness or cortical volumes (but there is no reason that the results would change just with reprocessing one hemisphere with the same freesurfer version). Let me know how it goes, Marie Quoting Christian Scheel <demi_...(a)gmx.net>: Dear all, I have successfully run 'recon-all -lgi' for all my subjects. However the computation process stopped in one of the brains claiming an lGI vertex value was aberrantly too high and giving me the following error message: ##### ... remeasuring lGI value for vertex iV = 32501. It may take a few minutes. WARNING -- Problem for vertex iV = 32501, lGI value is aberrantly high (lGI=40.5282)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/home/freesurfer/christian/34/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! ##### I have already restarted the computation twice without success. The script always crashes at the same vertex. The error message and the wiki page mention such an error in connection with possible topological defects. However when I check the mris_euler_number for the subject's rh.pial it interestingly does not show me any topological defect. Here is the output: ##### [freesur...@localhost ~/christian]$ mris_euler_number /home/freesurfer/christian/34/surf/rh.pial euler # = v-e+f = 2g-2: 133775 - 401319 + 267546 = 2 --> 0 holes F =2V-4: 267546 = 267550-4 (0) 2E=3F: 802638 = 802638 (0) total defect index = 0 ##### In all other brains the lGI calculation was successful. Does anyone of you have an idea? Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry -- Jetzt 1 Monat kostenlos! GMX FreeDSL - Telefonanschluss + DSL für nur 17,95 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a

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mri_watershed error
by Kathy Zhang 09 Feb '09

09 Feb '09

Hello all, I've been working with a set of about 200 brains, and in 19 of these I'm getting the error "mri_watershed Error: GLOBAL region of the brain empty !". I've checked the talairach transformation with tkregister2, and in 17 of those cases, the transformations look fine (the two other cases were just bad scans). I'm using freesurfer version 4.0.5 for linux, and have already tried previous suggestions to run a skull strip off orig.mgz and checking the FOV values on T1.mgz and orig.mgz. Does anyone know what I could do to fix this error or somehow work around it to continue the skull strip? Thanks, Kathy Zhang

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dt_recon
by Siddharth Srivastava 09 Feb '09

09 Feb '09

Hi everyone, I have recently started using the dt_recon processing pipeline in freesurfer. I just ran a dataset through it, and had a few questions about the methodology 1) How does the script calculate the mask from the DW data set. Is there any way to influence the mask calculation routine? I am familiar with bet/bet2 and i have an set of parameters tuned to my dataset. within dt_recon, i get the entire volume as a mask, while fsl generated a nice inclusive mask. Is there any way i can use the bet generated mask with dt_recon? 2) why is a glm fit done at the end of the processing stage? best regards, sid.

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"preproc-sess" failing at 3dvolreg
by Krishna Srihasam 09 Feb '09

09 Feb '09

Hi, I am trying to analyze my fMRI data ( collected at MGH) using FSFAST and I was following the tutrial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastWorkFlows) I was able to unpack the data. But when I run "preproc-sess -s <subject_name> -fwhm 2", it fails at 3dvolreg. Here is the log file fmc.nii.mclog. I checked the tempvol.nii.gz . afni was able to open it and disply the slice. Any help is welcome. regards, krishna /tmp/sk/FSFAST/abe_090116/bold /usr/local/imports/freesurfer/fsfast/bin/mc-afni2 --i 005/f.nii --t 005/f.nii --frame 0 --o 005/fmc.nii --mcdat 005/fmc.mcdat Thu Jan 22 19:07:38 EST 2009 uid=2308(sk) gid=12308(sk) groups=11(floppy),17(audio),18(video),19(cdrom),12308(sk),12345(spm),12349(numbra) ives Linux ives 2.6.24.5-smp #2 SMP Wed Apr 30 13:41:38 CDT 2008 i686 Intel(R) Xeon(R) CPU E5405 @ 2.00GHz GenuineIntel GNU/Linux /usr/local/imports/freesurfer/bin/3dvolreg mcdat file is 005/fmc.mcdat tmp dir is 005/tmp.mc-afni2.15217 #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float nskip = 0 ndrop = 160 $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... Dropping last 160 frames writing to 005/tmp.mc-afni2.15217/tempvol.nii.gz... #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... writing to 005/tmp.mc-afni2.15217/invol.nii.gz... #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold 3dvolreg -verbose -dfile 005/fmc.mcdat -base 005/tmp.mc-afni2.15217/tempvol.nii.gz -prefix 005/tmp.mc-afni2.15217/outvol.nii.gz 005/tmp.mc-afni2.15217/invol.nii.gz ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ** ERROR (nifti_image_read): failed to find header file for '005/tmp.mc-afni2.15217/tempvol.nii.gz' ** Couldn't open -base dataset 005/tmp.mc-afni2.15217/tempvol.nii.gz ERROR: 3dvolreg

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adding uncached variable to qdec
by Juranek, Jenifer 09 Feb '09

09 Feb '09

Hi, Running FSv4.2.0 on RHEL4. I'd like to add a variable such as lgi to qdec analyses. I created a .Qdecrc and .fsgd file, ran the lgi files through mris_preproc & mri_surf2surf (following instructions for Uncached Data posted under Group Analysis of the FsTutorial). While the output of mri_glmfit displays nicely in tksurfer, I'd like to look at the data within qdec (where scatter plots are easily viewed). The error I receive within qdec is as follows: <1st subject in fsgd file>/surf/?h.<var_name>.fwhm<smoothing factor>.fsaverage.mgh does not exist Is there an easy (e.g. scripted) way to generate the files within each subjects' /surf dir for a new variable not already recognized by the -qcache script for use by qdec? Many Thanks for any suggestions/solutions, Jenifer

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SPM Issues
by Dave Brohawn 09 Feb '09

09 Feb '09

Hello, I am having issues with SPM Register-Sess and I am not sure why. The command I am entering and the response I receive are spmregister-sess -s FB11059A -------------------------------------------------------------- spmregister-sess logfile is /autofs/space/seymour_001/users/folate_subjects/log/spmregister-sess.11485.log -------------------------------------------------------------- Session: /autofs/space/seymour_001/users/folate_subjects/FB11059A ---------------- Fri Feb 6 11:43:07 EST 2009 Detected format at nii Log file is /autofs/space/seymour_001/users/folate_subjects/FB11059A/bold/011/spmregister.log Fri Feb 6 11:43:07 EST 2009 --s FB110059A --mov /autofs/space/seymour_001/users/folate_subjects/FB11059A/bold/011/f.nii --reg bold/register.dat --fsvol brainmask $Id: spmregister,v 1.21.2.3 2008/07/07 13:53:49 greve Exp $ matlab matlab ERROR: /space/seymour/1/users/folate_subjects/FB110059A/mri/brainmask.mgz not found in either COR or MGZ formats ERROR: spmregister failed The pre-proc command worked, and brainmask construction was completed successfully. In fact, I can go into this subjects mri folder, and see the brainmask.mgz file. Here is the bugr information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0-20090203 RedHat release: CentOS release 4.6 (Final) Kernel info: Linux 2.6.9-67.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects Thank you, Dave Brohawn

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Work with MRI and PET simultaneously
by Rafa x 09 Feb '09

09 Feb '09

Hello FS team, I would like to know if it's possible to load a PET image in tkmedit and tksurfer, and overall I need to know if I can coregistrer a PET image with a MRI (of the same patient). I have the tags of the cortical segmentation generated by recon2 based on the MRI and I want to work with them in the PET. Is it possible? How? Thank you very much

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tksurfer to tkmedit orientation
by Thomas Wallis 08 Feb '09

08 Feb '09

Hello, I have recently started using freesurfer for reconstruction. If I note the Talairach coordinate of a vertex in the left hemisphere in tksurfer, then enter this coordinate into tkmedit, the point appears on the right of the image (i.e. in the "right" hemisphere). That is, the "left hemisphere" generated by autorecon2 seems to correspond to the right side of the image in tkmedit, and vice versa. Is this as it should be, or have I made a mistake somewhere? I couldn't seem to find anything documenting this in the wiki. Or am I being stupid? Thanks in advance for your help. Tom Wallis

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Re: [Freesurfer] creating label for dlpfc
by Prapti Gautam 07 Feb '09

07 Feb '09

Thank you for your help, I have incorporated parts of the regions that would normally include gyri and sulci of the superior frontal, middle frontal as well as inferior frontal in the aparc.a2005s atlas. I've decided to define it according to Raz et al 1997 :Cereb Cortex. 7(3):268-82 & Raz et al 1999 :Psychol Aging. 14(3):436-44 Prapti -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Saturday, 7 February 2009 5:29 AM To: Prapti Gautam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating label for dlpfc How are you defining dlpfc? I've been looking into this myself recently, and it has not been all that clear. Randy Gollub has recently put a lot of effort into it. As Nick describes, you can draw it on one and transfer it to another. I've been combining $hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label from the aparc.a2005s atlas. Seems pretty good. doug Prapti Gautam wrote: > > > > Dear all, > > > > I am trying to measure the volume of the dorsolateral prefrontal > cortex in a large group of subjects. I have created a new label that > only includes the dlpfc for a subject but realised that the same label > file cannot be used on another subject. Has anyone created a > customised ROI for dlpfc to use in a group of large subjects or can > point me in the right direction ? The only other option I know is to > individually create a label file for each subject which would be very > time consuming. > > > > Thanking you in advance, > > Prapti > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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updated ReconAllFilesVsSteps spreadsheet?
by Sam Torrisi 07 Feb '09

07 Feb '09

Hi Freesurfers- another newbie question: would updating this to ver. 4.2 result in significant changes? would the rest of the community benefit? http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps and of course would it also be a pain to do? it's just that some of us don't know python thanks! -Sam Torrisi UCLA, Neuroscience IDP

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Freesurfer February 2009