Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Running mri_glmfit-sim with pre-computed Monte-Carlo
by Thomas DeRamus 21 Oct '14

21 Oct '14

Dear Freesurfer Experts, I have a label file of a number of ROI's I've made based on a mask. I'm trying to get an idea of what cluster are significant within a focused region of the label file. To make the correction a little less sever, I pre-computed some monte-carlo values using mri_mcsim mri_mcsim --o /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain --base mc-z --surface fsaverage rh --nreps 10000 --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask mri_mcsim --o $SUBJECTS_DIR/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain --base mc-z --surface fsaverage lh --nreps 10000 --label $SUBJECTS_DIR/fsaverage/label/lh.SocialBrainMask Respectively for each surface (the labels are different on each hemisphere). I've run mri_glmfit and have the uncorrected outputs and results (there are actually 6 of these, one for volume, thickness, and surface area for each hemi): mri_glmfit --y rh.diagnosisxagexrightThickslopetest.thickness.10.mgh --fsgd SBM_glmRightthickNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agethickness.glmdir But when I try to do the mri_glmfit-sim, I am having trouble getting it to read in the corrected csd file. I'm wanting to run it at cwp of 0.05 at a threshold of 2 (0.01), with a correction for two hemispheres. However, when I try to run it with --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain , it has trouble understanding the --cwp .05, --2spaces and 2 abs (after cache dir) flags. Additionally, it wants a --sim and --sim-sign value like it wants to compute a monte-carlo from scratch. Could I get an example on how best to direct it to the simulation I've run on it? Thanks much. -Thomas -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpderamus(a)gmail.com, faustus(a)uab.edu

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mri_volcluster problems
by Joo Tan 21 Oct '14

21 Oct '14

Hi I have a few questions regarding the use of “mri_volcluster” for clusterwise thresholding. Essentially, we have a volume of pvalues obtained from a two tailed t-test comparing beta values from condition A vs condition B. When I ran this command: mri_volcluster --in transformedP.nii --sum cwthres_sum.txt --sign abs --fwhm 6 --mask avgmas.nii --cwpvalthresh 0.05 --thmin 2.3 --cwsig cwthresclusters.cwsig.nii I got this error message: ERROR: you must specify a pos or neg sign with --fwhm Input was –log10(p-value) Thmin was –log10(primary p threshold) Is there a way to perform clusterwise thresholding on results from two tailed tests? Is it essential to use –log10(p) values as input? Can I use raw t-values or any other values as input and thmin instead? Finally, are there any papers/references which this command is based on? Many thanks!

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unpacksdcmdir
by Alshikho, Mohamad J. 21 Oct '14

21 Oct '14

Hi , The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs? Thanks, Moahmad

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Do not have 'recon edit' button! Please help!
by Smaragdi A. 21 Oct '14

21 Oct '14

Dear mailing list, I am really stuck here.. Please can someone tell me why I cannot find the recon edit button on freeview! I am not sure if the version of Freesurfer I have downloaded is old, or I have done something wrong, or I am just blind.. But I cannot find the 'recon edit' button in freeview (see attached screenshot). What am I not doing right? Many thanks, Areti

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skewed CT viewed in tkregister2
by Borzello, Mia 21 Oct '14

21 Oct '14

Hi Freesurfers I'm having trouble viewing a CT in tkregister2. Here is the output from bugr: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri 1. BI20 2. tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3. the coronal/saggital/horizontal views were skewed 4.attached. Thanks a lot, Mia

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T1 white matter segmentation
by Alshikho, Mohamad J. 21 Oct '14

21 Oct '14

Hi FS Experts, The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2 I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

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GLM contrast vector for continuous variable interaction
by Bronwyn Overs 20 Oct '14

20 Oct '14

Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, & sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Parenchyma/CSF
by Mahmoud 20 Oct '14

20 Oct '14

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud

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(no subject)
by Mahmoud 20 Oct '14

20 Oct '14

1 0

Re: [Freesurfer] adding time points to longitudinal base template
by Martin Reuter 20 Oct '14

20 Oct '14

Hi Koushik, no, I cc the list, maybe someone has done tests or seen papers. I read somewhere on atlas construction, that 10 images are fine, but that is cross subject. Here we only have small changes within subject, so from my experience less are fine , BUT - 2 of course are not enough: in 2 the method is actually different (as the median in 2 is simply the average) . Starting with 3 a median intensity even exists for each voxel. - adding 1 new to 5 existing may work without sacrificing too much bias, but adding 10 to 5 is not a good idea. Also if the one that is added is very different from the first 5 (e.g. first 5 within a week, next 3 years later), then that will be problematic also. Best, Martin On 10/20/2014 12:07 PM, Govindarajan, Koushik Athreya wrote: > > Hi Martin, > > How are you? We had this below email conversation in March about > the longitudinal template and it's stability. You had mentioned that > with 5 time points, my template should be stable enough to patch > another timepoint. I have another study that has only 2 time points > and I was reading through your 2012 Longitudinal analysis paper that > had used 2 time points to compare with cross-sectional data. I was > wondering if you had any suggested literature for the number of time > points needed for stability of a template. > > Thanks > > Koushik Govindarajan > > *From:*Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > *Sent:* Friday, March 14, 2014 9:31 AM > *To:* Govindarajan, Koushik Athreya; freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] adding time points to longitudinal base > template > > Hi Koushik, > > there is a way to add time points without recreating the base: > recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all > > This is what the recon-all help says about that: > "If a new timepoint needs to be added to a longitudinal run where a > base subject > has already been created (from prior timepoints), then the -addtp command > can be added to the -long command in order to 'fix-up' the longitudinal > stream to accept the new timepoint. Note that the base subject is *not* > recomputed using the new timepoint. This potentially introduces a > bias, and it > is recommended to NOT add a time point this way! Instead recreate the base > from all time points and run all longitudinals again." > > So it's up to you. But given you already have 5 time points in your > base and add only 1, you may be fine. The base should be pretty stable > with 5 and if the 6th is not too different, it should not matter much. > I don't think anyone has ever done a thorough analysis about adding > time points. > > Best, Martin > > On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: > > Dear FS experts, > > I have a serial study in which I have run > cross-sectional and longitudinal analysis on 5 time points. Now, I > want to add a 6^th time point to my dataset. Do I have to rerun my > base template creation step from scratch or is there a way to just > add further time points to an existing template? > > Thanks > > Koushik > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu…> > > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > reuter(a)mit.edu <mailto:reuter@mit.edu> > Web :http://reuter.mit.edu <https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip…> > > 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. > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Freesurfer October 2014