Freesurfer

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30132 discussions

FS-FAST modeling question
by Benjamin Matthew Deen 04 Sep '11

04 Sep '11

Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 Any idea what might be going wrong, or how I can get this to work? Thanks, Ben

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what is thalamus-proper and clusters-table related question
by Tetiana Dadakova 04 Sep '11

04 Sep '11

Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs column: is it the number of vertexes in cluster? What kind of information can I get from this value? If two clusters have different areas but the same number of vertexes, does it mean something? Thank you very much for your help and for your time, Tanja.

4 6

dcm2nii and recon all
by Carolina Valencia 02 Sep '11

02 Sep '11

Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina

3 2

Surface analysis FSL GFEAT results for multiple subjects with 4 runs each
by Michelle Umali 02 Sep '11

02 Sep '11

Hi Freesurfers, I've been looking at the wiki for information on doing an surface analysis using GFEAT results for within subject, across multiple runs. On the wiki, a fixed effects analysis was used because there were only two runs. I have four runs and FSL uses FLAME 1 and FLAME 1+2. 1. Should/how do I do I random effects for 4 runsb? 2. How does one do a group surface analysis this for multiple subjects who each have 4 runs? Thanks. Michelle

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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

2 1

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

2 1

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?

1 0

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

2 1

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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