Freesurfer

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30084 discussions

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

2 1

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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Missing some parcellations
by Jürgen Hänggi 07 Feb '09

07 Feb '09

Dear FS experts There are 94 surface labels listed in the surface_labels.txt file in the FS home directory. However, when using aparcstats2table with the --parc option aparc.a2005s there are only 78 parcellated areas per subject reported in the list. Why? Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Fwd: transforms/talairach.xfm ***FAILED***
by roberto toro 07 Feb '09

07 Feb '09

Dear Freesurfers, I haven't been able to run recon-all in a set of subjects. All them stop at the point of the talairach transform verification. I uploaded one of the files here (5.3MB): http://dl.getdropbox.com/u/74925/20070404.nii.zip For that volume, the transform.xfm file looked indeed odd (m22=7.2??): 1.39488649 0.08332049 0.01164643 3.51684260 -0.14383204 7.20834160 -2.21084833 11.16247082 -0.16614650 1.02134335 1.85208952 -45.74753189 Using flirt (flirt -in 20070404.nii -ref MNI152_T1_1mm -out 20070404trans.nii -omat 20070404trans.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear), the transformation was: 1.05366 -0.050378 0.0606504 4.05766 0.0446432 1.09476 0.1321 -28.652 -0.058117 -0.180136 1.09158 31.7066 0 0 0 1 The voxel size of the volume is 1.17x1.17x1.2, so it shouldn't be a problem of resolution. When I converted the volume to mgz (mri_convert 20070404.nii mri/orig/001.mgz), the orientation was wrong; but changing it using the Volume Tools in tkmedit did not alter the outcome... Finally, I also used the --notal-check switch in recon-all, but then the script failed before completing skull stripping... thank you very much in advance for your help! roberto

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ventricles in wm.mgz volume
by Derin Cobia 07 Feb '09

07 Feb '09

We're experiencing some difficulties with editing several of our control subjects' wm.mgz volumes. For many of them the ventricle space was not filled during the recon-all process (some subjs have enlarged ventricles, while others do not). Re-running with the - bigventricles flag did not correct the problem, and we subsequently filled the space manually by added new voxels (255 value) in the wm.mgz volume. After running them again under -autorecon2-wm, we discovered that the wm.mgz volumes now appear without any of our edits (as if they had been run with a -clean-wm flag). We edited and reran again, but with the exact same result for a second time, but only for a subset of the original (edits worked on some, didn't on others). Any thoughts as to why this is occurring? We are pretty confident that the volumes are saved each time edits are made, and we are not running with any -clean flags. If all else fails, is it permissible to using the subjects as is (see attached pics) if the surfaces being affected are only the 'unknown' regions? FS 4.1.0 is the version that is being used, thanks. -Derin

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SPM Register Issues
by Dave Brohawn 06 Feb '09

06 Feb '09

1 0

labels for atlas
by amyr＠nmr.mgh.harvard.edu 06 Feb '09

06 Feb '09

Hi All, I have created labels (and annotation files) for just the ventro-medial pre-frontal cortex. I would like to create an atlas based on my manual labels. Do I need to create another label "other", that includes the rest of the surface, before I can create the atlas? Thanks for your help. Amy Raudenbush

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