Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Grad_Unwarp question
by Mohana Ramaratnam 02 Sep '11

02 Sep '11

Hello, We used to run: grad_unwarp with matlab invoked with -nodisplay option. The version information on this file is: version: Version for distribution, 1.0, author: SC----------- id: id9/01 13:34:11 I see that Freesurfer 5.1 has a grad_unwarp script, which I can modify to invoke matlab with -nodisplay, however, I dont see any sub-folder grad_unwarp_tables in FREESURFER_HOME. Where do I get these tables from? Am I missing some installation option? Regards Mohana

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Longitudinal aseg errors
by Jeff Sadino 02 Sep '11

02 Sep '11

Hello, I finished processing my first longitudinal subjects, but I have some errors. The TP3.long aseg.mgz file is poorly segmented (corpus callosum, see attachment). I am wondering where I should make edits to correct this. The surfaces of all 3 longitudinal timepoints look fine, so according to the wiki, I should only have to edit the TP3.long. Is that true? If not, then I will have to edit TP3.cross. Originally, the watershed for TP3.cross was bad. I edited this and re-ran autorecon2 and autorecon3, and exited with no errors. However, the cross aseg.mgz is still bad. I thought maybe the talairach.m3z file was bad, but the nu_noneck image was transformed fine. I see that the log file says during the mri_ca_label step that the CSF peak is too bright - rejecting (see attachment). After comparing the csf areas of the TP3.cross norm image with the csf areas of the TP1.cross norm image, they have values of 30 compared to values of 10. Previous posts have suggested to copy the orig.mgz image to the nu.mgz image for a similar problem. Can someone please advise me on where it would be best to make the edits so that my longitudinal reconstructions are accurate? Thank you! Jeff Sadino

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Freesurfer 4.20 for recon-all –all, and Freesurfer 5.10 for recon-all -s <subjid> -qcache? Workaround for a bug in the group statistics for volume?
by Knut J Bjuland 02 Sep '11

02 Sep '11

Hi I have two questions about the Freesurfer recon-all. Can I use Freesurfer 4.20 for recon-all –all, and Freesurfer 5.10 for recon-all -s <subjid> -qcache? There was also reported a bug in the group statistics for volume in Freesurfer 5.1. Are there any workaround for this error?

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thalamic segmentations in freesurfer
by Ritobrato Datta 01 Sep '11

01 Sep '11

Hello All, I noticed the following in FreeSurferColorLUT.txt 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 Are these generated by the cross-sectional recon-all or are these futuristic ? If they are available how do I view them ? Please let me know. Thanks Ri

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File correction during NIFTI conversion
by Antonella Kis 01 Sep '11

01 Sep '11

Dear FS experts, While doing a NIFTI conversion for my dicom files I tried near mri_convert the MRIcron conversion. I saw that during this conversion the MRIcron is doing a correction and image orientation such that one of my final NIFTI file is having a smaller size that the NIFTI file coming out from the mri_conversion. It is OK to use this smaller size or not for my further analysis? I wonder if is very different than the one from mri_convert. Thank you for your advise. AK

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Re: [Freesurfer] (no subject)
by Douglas Greve 01 Sep '11

01 Sep '11

That actually looks fine to me too. When FEAT creates a mask of the brain, it extends the mask out a bit to make sure that it does not cut off any brain. Every voxel in the mask will get a zstat. If your raise the threshold a bit, the stuff outside of the brain will probably drop away. doug On 8/31/11 6:10 PM, noam Schneck wrote: > Sure thing, attached to this email are two sets of images. One > includes the tkregister2 outputs in which the movable is the example > func. Based on the surface the registration looks good. The other > image is the zstat from that same run (in EPI space) overlayed onto > the anatomical using the same registration matrix that I used in the > tkregister2 output (this is seen in the tkmedit output). What you can > see is that the zstat activation map extends outside of the brain and > skull, despite using a registration matrix that produced a good > registration when just looking at the grey white matter boundary. if > it would be helpful I can also send you images of what the > example_func overlayed onto the anatomical in tkmedit looks like. It > basically shows that the examplefunc extends outside the borders of > the skull. I would have included it but it exceeds the email KB limit. > > Thanks so much for taking the time, > noam

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hippo-subfield on longitudinally processed brains
by Wenger, Elisabeth 01 Sep '11

01 Sep '11

Dear freesurfer specialists, I am trying to run the very interesting hippocampus subfield segmentation on subjects that have already undergone the standard volumetric pipeline AND the longitudinal pipeline. I tried the command "recon-all –subjid <myid> -hippo-subfields". Unfortunately, i'm getting the following output message: "ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists." Can I just run the -hippo–subfields command on the already longitudinally processed brains, and simply include the flags "-long <tp1id> <templateid>" (without "-all") so freesurfer can use the long-directory as output (as it states in the error message)? Or do I have to run the -hippo–subfields command on the crosssectionally processed brains and include the flags "-long <tp1id> <templateid>"? Do I then also need to include the flag –all so that it will do the whole longitudinal processing again? Thank you very very much for your help! Cheers, Elisabeth ******************************* Dipl.-Psych. Elisabeth Wenger Predoctoral Research Fellow Center for Lifespan Psychology MPI for Human Development Lentzeallee 94, 14195 Berlin, Germany phone: +49-30-82406-427 web: http://www.mpib-berlin.mpg.de<http://www.mpib-berlin.mpg.de/>

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Tracula time estimates
by Bill Taylor 01 Sep '11

01 Sep '11

I looked at the wiki and the FAQ but still need an answer. In my work to get more of Freesurfer available to researchers using our cluster, I am concerned about the 48+ hours for a run on one subject. Our 1700 slots which can run these jobs only promise a 24 hour time slice before evictions. Is it likely that all three steps will fit within a 24 hour time frame. What are the outside limits for: Pre-processing FSL's bedpostX Reconstructing white-matter (WM) pathways If they run over, is it possible to due the part which runs over in pieces? Thanks in advance! There are currently 3 groups on campus interested in our automation involving thousands of scans. -- Bill Taylor 608-263-2656 (cell 608-219-4430) Center for High Throughput Computing(CHTC) Condor project Computer Sciences University of Wisconsin, Madison

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Renaming a processed subject
by Irwin, William 01 Sep '11

01 Sep '11

Hi For purposes of de-identification, is there an easy way to "rename" all the contents of data for a processed subject? For example, If I want to do share data or do reliability training on an existing subject (e.g., "ABC1234"), I want to rename everything associated with this case to "Case1". Thanks Wil ____________________________________ William Irwin | Imaging Core Supervisor UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wirwin(a)memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816

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calculating GM and WM surface-based volumes
by Alexopoulos, Dimitrios 01 Sep '11

01 Sep '11

I have generated surfaces using the the centos4 build (version 5.0) and want to confirm that my surface-based GM and WM volumes are correct. For the surface-based GM calculation I originally used 'mris_anatomical_stats -l lh.cortex.label subjectID hemi' (run from within the 'label' subdirectory) and for WM i used 'mris_wm_volume subjectID hemi' (run from within the 'surf' subdirectory). When I add the left/right cortical volumes, I get a total that is different from what is output in the 'aseg.stats' file, which in version 5.0 is noted to contain total surface-based GM volume. (Cortex, CortexVol: Total cortical gray matter volume (based on surface-stream). What are the correct GM and WM surface-based volumes? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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