Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Reposting: Clusters by Multiple comparison
by Douglas N Greve 08 Feb '12

08 Feb '12

What I have listed as fa.nii.gz should be the same file that you passed to mri_glmfit with the --y option. doug Antonella Kis wrote: > Dear Doug, > > THANKS SO MUCH for your help. My last questions is: I suppose the --i > fa.nii.gz is an input file. What should be my input in thi scase if > for each subject I have different fa values and gor the mri_glmfit I > used the GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz which is the > concanetated masked file resampled to the CVS space. Should I use this > file or what exactly for the fa.nii.gz? > > Also will mri_volcluster but it will give the correct clusters if I am > not mentioning the --reg option? > > MAny thanks and have a great day! > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, February 8, 2012 1:50 PM > *Subject:* Re: Reposting: Clusters by Multiple comparison > > Oh, ok, I remember this now. Yes, you can use your mri_volcluster > command below the clusters. To get the table, run > mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz > --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary > > The fa.avg.dat will have a table of data. Each row will be a subject, > each column a cluster (matching that found in permcsd.sig.cluster.summary) > > doug > > > Antonella Kis wrote: > > > > > > Hi Doug, > > > > Thank you very much for your help. I attached the log file. I can > get the clusters summary if I run the mri_volcluster but it will give > the correct clusters if I am not mentioning the --reg option? > > Also, when I am visualizing my clusters using tkmedit: > > > > tkmedit cvs_avg35 norm.mgz \ > > -ov > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh > \ > > -seg > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh > \ > > > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut > \ > > -fthresh 0.2 -fmax 1 > > > > I can read the functional value for each cluster. What exactly this > value represents? Is my FA value or -log10(p)? > > > > How can I get my FA values within each cluster in a table? > > > > > > > > Thank you so much. > > Antonella > > > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, February 8, 2012 11:37 AM > > *Subject:* Re: Reposting: Clusters by Multiple comparison > > > > Hi Antonella, the right way to do it is to figure out what is going > wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you > send the log file? Should be permcsd.mri_glmfit-sim.log. If you need > to run it for debugging purposes, you can run it with 10 iterations > (change permcsd to permcsdtmp so you don't overwrite what is there). > This should produce all the files, so if something is not there, it > should be easy to track down why. > > doug > > > > Antonella Kis wrote: > > > > > > > > > Dear Doug, > > > > > > When I run the: > > > mri_glmfit-sim \ > > > --glmdir GroupAnalysis_pos.glmdir \ > > > --sim perm 10000 3 permcsd \ > > > --sim-sign pos \ > > > --cwpvalthresh .05 > > > > > > I am not getting my clusters file permcsd.sig.cluster.mgh with > the clusters summary so as you recommended I am running the > > > > > > mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask > Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn > Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 > --seg cvs_avg35 norm.mgz --csdpdf > Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd > Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig > Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh > > > > > > > > > My question is: it is OK if I am not mentioning any registration > or what should I input under --reg while I running the mri_volcluster > if my for DTI preprocessing I used the dt_recon which computes for > each subject an fa.nii and register.dat using the Talairach > registration and later I registered all my subjects on the CVS space? > > > > > > Thank you. > > > AK > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the sender > and properly > > dispose of the e-mail. > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Question about ?h.sulc and ?h.curv
by Jing Ming 08 Feb '12

08 Feb '12

Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! BestJing

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Re: [Freesurfer] Reposting: Clusters by Multiple comparison
by Antonella Kis 08 Feb '12

08 Feb '12

Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, February 8, 2012 11:37 AM Subject: Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: > > > Dear Doug, > > When I run the: > mri_glmfit-sim \ > --glmdir GroupAnalysis_pos.glmdir \ > --sim perm 10000 3 permcsd \ > --sim-sign pos \ > --cwpvalthresh .05 > > I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the > > mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh > > > My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? > > Thank you. > AK > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark
by Mark Fletcher 08 Feb '12

08 Feb '12

Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years data through the recon-all step while using version 5.0. Additionally, I made a substantial amount of corrections to many brain regions that I am hoping to not redo (with the number of subjects in my study it will take well over a month or two to re-do this). I collected my second years worth of data after 5.1 came out, and ran the recon-all on all of these subjects using version 5.1 of FreeSurfer. Similarly, I have already made corrections to this set of data as well. My ultimate goal is to now use the longitudinal processing stream. I think I understand the process, however, I am wondering if I need to re-do all of my corrections, or if I can salvage my corrections made from previous versions. I am a little concerned about what the -clean flag might do (will it eliminate my corrections?) Furthermore, while looking at your suggestions of editing errors, it says that you can "save time" because some changes only need to be made to the base. However, in my case, I think re-doing all of the edits will actually cost me much more time. I am willing to scrap all of my work if this is necessary, but I am wondering if there is a work-around. Sincerely, Mark

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Clusters by Multiple comparison
by Antonella Kis 08 Feb '12

08 Feb '12

Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK

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Visualising the FA group analysis results
by Antonella Kis 08 Feb '12

08 Feb '12

Dear Experts, I completed my FA group analysis and I expect my FA to be larger in controls versus patients (based on the uncorrected results). I corrected by multiple comparisons using: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 so I have my: permcsd.sig.cluster.nii – map of significance of clusters permcsd.sig.ocn.nii and grf.th3.pos.sig.ocn.lut – segmentation of significant clusters permcsd.sig.cluster.summary – text file of cluster table (clusters, sizes, MNI305 XYZ, and their significances) 1) How can I visualize my results more exactly how I can visualize my uncorrected and corrected results. 2) How I can output in a table the FA values corresponding to each cluster? 3) If use tkmedit is the Functional value given me the FA values while moving the cursor or this Functional value represents something else in the case I plot: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 Thank you very much, Antonella

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volume smoothing
by Klein, Holger 08 Feb '12

08 Feb '12

Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to ameliorate the smoothness of my volume but could not find a solution. Could anyone give me an advice to cope with that problem? Any help is greatly appreciated, Thanks in advance, Holger

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Verifying ICV in FS5
by Jeff Sadino 08 Feb '12

08 Feb '12

Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > It's hard to tell from the coronal, but it looks ok. The problem is more > visible in the sagittal. > > doug > > Jeff Sadino wrote: >> >> Hello Doug, >> >> I loaded up the tkregister2 program and I think I see some poor >> transformations. I've never really used it before though. Am I just >> looking at whether or not the green line lines up with the target image wm? >> Can you look at my pictures real quick? 040002_S04_test is from fs4 that >> is having problems. 040002_S04 is from fs3 and has a good icv value. Some >> of the blank spots are from my graphics drivers and unrelated to fs. >> tkregister2 also said the determinant of 040002_S04_test was 1.49544. >> >> Martin, >> >> Thank you for the idea. I did this, and got a much better icv. On fs3, >> where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. >> Using your idea on fs4, it was 1,819,485. >> >> Thank you so much to everyone for your help! >> Jeff >> >> On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec <martin.kavec(a)gmail.com >> <mailto:martin.kavec@gmail.com>> wrote: >> >> Hi Jeff, >> >> I see this relatively often. Eventhough the talairach registration >> is fine, the >> ICV is underestimated. In this case I take old ICV, which helps. >> >> mri_segstats --subject $MYSUBJECT --old-etiv-only >> >> This is in 99% of these cases a cure. This is not just a blind >> attempt. In >> these cases I then compare each ICV normalized aseg volume against >> an age >> matched group and only if the old-etiv-only ICV gives better >> estimates I use >> it. >> >> Cheers, >> >> Martin >> >> On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: >> > Thanks Doug. That is very good news to hear! >> > >> > Maybe I spoke too soon about fixing the problem. I looked at 4 more >> > subjects, and even though the icv value is unique, its magnitude >> seems >> > wrong. Often times, it is smaller than the BrainSegVol, which >> doesn't make >> > much sense and it is also low overall. >> > >> > >> > # subjectname 090167_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1639959, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1639959.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1289194.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1299686, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1299686.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1105595.114652, mm^3 >> > >> > # subjectname 090182_S01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1599981, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1599981.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1199694.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1205382, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1205382.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1114008.197334, mm^3 >> > >> > # subjectname 090187_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1826694, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1826694.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1381871.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1388801, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1388801.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1307759.303915, mm^3 >> > >> > # subjectname 100014_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1948121, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1948121.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1467582.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1488088, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1488088.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1637915.031593, mm^3 >> > >> > # subjectname 040002_S04_test >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1774481, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1774481.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1288022.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1312132, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1312132.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1302696.178406, mm^3 >> > >> > I had also done 040002_S04 in fs 3.0.5, and this is the result: >> > # subjectname 040002_S04 >> > # BrainMaskFile mri/brainmask.mgz >> > # BrainMaskFileTimeStamp 2008/29/08 15:44:46 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1753272, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1753272.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1310474, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1310474.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1767481.547316, mm^3 >> > >> > All of the values are similar except the icv. Do you guys have >> any ideas >> > where I can look for the answer? >> > >> > Thank you very much, >> > Jeff >> > >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >

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mris_divide_parcellation
by Yolanda Vives 08 Feb '12

08 Feb '12

Dear Freesurfer experts, I have a question regarding mris_divide_parcellation. I have created a file containing the parcels from aparc.annot that I want to split and I have run the following command. Why is Freesurfer allocating 36 additional units? When I open the new annotation file (rh.aparc.splitted) with matlab (using read_annotation), I can see that at the end of colortable.struct_names there are a lot of parcels called "cluster38, cluster39, ..., cluster71". What are exactly these clusters? Many thanks, Yolanda *In splittable.txt* file precentral 2 *Command* ./mris_divide_parcellation fsaverage rh aparc.annot splittable.txt rh.aparc.splitted *Output* reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) interpreting 4th command line arg as split file name dividing precentral into 2 parts allocating new colortable with 36 additional units... saving annotation to rh.aparc.splitted writing colortable into annotation file...

2 2

autmatic image with panel of hemisphere made by script
by Knut J Bjuland 08 Feb '12

08 Feb '12

I have used Tksurfer to make image from cross subject statistics maps in mgh files. Is it possible to use a script to make image with both hemisphere in lateral and medial view. I would also like to display p values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How can I produce image with 500 dpi in tksurfer? Knut J

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