[Freesurfer] FreeSurferColorLUT labels
Hi, In FreeSurferColorLUT.txt (Freesurfer 5.1), there is a label for the inferior colliculus (7100), but this structure seems only to be labeled collectively with other brainstem structures (16) in aparc.a2009s+aseg. It appears from posts in the mail list that only a subset of the labels in FreeSurferColorLUT.txt make it into the automatic segmentation done by recon-all. Any suggestions of how I could access lh and rh inferior colliculus labels for fsaverage, and then morph them to each subject's norm.mgz? Thanks, Susan McLaughlin SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] FDR threshold on functional data
Hi, I am looking at functional group surface data analyzed with mri_glmfit in tksurfer (using Freesurfer 4.1). I would like to threshold using FDR - but only within a specified label - and then see the resulting functional data map. Once I have the functional dta loaded as an overlay, I have been loading my label and marking the selected label under the Tools menu. I then set the threshold using FDR only on marked data. So far, so good. However, once this is done, I have not been able to see the thresholded functional map in the label; I can only the whole area in white, marked. How do I see my functional data map? I apologize for this simplistic question; I have not been able to find a solution looking through the tksurfer guides online or the mail archives. Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Trouble performing Monte Carlo simulation constrained to label
Hi, I am trying to run a Monte Carlo simulation on functional data constrained to a label using Freesurfer 4.0.1. I did not use Qdec for data analysis. Looking at a previous post - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html - I see that I should: 1) constrain when running mri_glmfit, then 2) use mri_glmfit-sim (as opposed to running mri_glmfit with the simulation options). I have done step 1, however when I try to mri_glmfit-sim, I receive a command not found message. Is mri_glmfit-sim not available in 4.0.1? Can I copy a workable version of mri_glmfit-sim into 4.0.1? Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Monte Carlo
Hi Doug, I am trying to run a Monte Carlo simulation on functional data constrained to a label. Looking at a previous post - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html - I see that your advice is to 1) constrain when running mri_glmfit, then 2) use mri_glmfit-sim rather than running mri_glmfit with the simulation options. I have done step 1, however when I try to mri_glmfit-sim, I receive a command not found message. I confess that I am running an old version of Freesurfer (v 1.133.2.5). Is this my problem? If so, will it be a problem if I run mri_glmfit with the simulation options? Thank you and happy holidays, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] functional ROI analysis
Hi Doug, Thanks for your helpful answer (below) with respect to the use of mri_segstats on functional activation in subject-specific ROIS. I have a follow-up question, however, regarding the initial creation of the ROIs. I am basing my ROIs on the Desikan-Killiany atlas, either using existing labels in the atlas or sometimes splitting them into anterior and posterior. I tried making the ROis 2 different ways, and found I got different results. 1) If I make an ROI by selecting or drawing D-K atlas regions on fsaverage, then morph it to each individual’s surface with: mri_label2label --srcsubject fsaverage --srclabel /Applications/freesurfer/subjects/fsaverage/label/[ROIname].label --trgsubject [subj] --trglabel /Applications/freesurfer/subjects/[subj]/label/[ROIname].label --regmethod surface --hemi lh and then – to go from the surface (.label) to the volume (.nii): mri_label2vol --temp example_func.nii.gz --reg reg/freesurfer/anat2exf.register.dat --proj frac 0 1 .1 --hemi lh --label /Applications/freesurfer/subjects/1012/label/[ROIname].label --subject [subj] --o [output name].nii then I get a fully contiguous region when I view the ROI on the individual’s surface or more total voxels when I look at a summary of the ROI characteristics using mri_segstats. 2) If I instead make the ROI using: aseg2feat –feat [subj].feat --aseg aparc+aseg and then fslmaths [subj].feat/reg/freesurfer/aparc+aseg.nii.gz –thr [label # of pertinent region] –uthr [label # of pertinent region] [subj].feat/reg/freesurfer/[ROIname].nii.gz then I get a chopped up, non-contiguous region with fewer total voxels. My plan therefore is to use Method #1 above, but I want to make sure this is OK: that I'm not somehow including spurious voxels that have somehow been incorrectly generated by going from surface to volume. Am I OK with Method #1 above? Thanks again, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington On Mon, 26 Nov 2012, Douglas Greve wrote: Hi Susan, ok, I see what you are doing now. Let's do it this way: 1. First transfer your label to the volume: mri_label2vol --temp example_func.nii --reg anat2exf.register.dat --proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii 2. Then run segstats: mri_segstats --i cope2.nii --seg yourlabel.func.nii --mask zstat1.nii --maskthresh 2 --masksign abs --o sum.dat The cope and the zstat are now volumes. doug On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote: Hi Doug, Thanks for the quick answer. Sorry to be dense, but does this need somewhere to include registration matrix, anat2exf.register.dat, to register to the subject's surface? And at this point in the analysis, the feat folder does not include copes and zstats separated out by hemisphere, although there are zstat[#].surf.lh.w and .rh.w files in the main feat folder. Again, sorry for my limited understanding of file structure. Susan On Mon, 26 Nov 2012, Douglas N Greve wrote: Hi Susan, you can't use func2roi-sess. You'll have to put together some commands, but it should not be too hard, something like mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat where zstat1 is your all/nothing contrast sampled onto the surface and cope2 is some other contrast sampled on the surface. You can do this for each subject, then run asegstats2table giving it paths to all of your sum.dat files doug On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote: Hi, I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat. Is there any way to pass my original analysis into func2roi-sess? I tried using: func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d but get ERROR: cannot find any sessions. Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface. Thanks in advance for and advice or suggestions. Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N
[Freesurfer] functional ROI analysis
Hi, I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat. Is there any way to pass my original analysis into func2roi-sess? I tried using: func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d but get ERROR: cannot find any sessions. Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface. Thanks in advance for and advice or suggestions. Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] resending question about 3rd level analysis
Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc. I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using: mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label However, I want to use a random as opposed to fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysis, do I need to correct for multiple comparisons? Many thanks in advance, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] 3rd level surface analysis of fMRI data
Hi,I’m a Freesurfer novice, and am confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc.I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using:mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.labelHowever, I want to use a random effects rather than fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysi! s, do I need to correct for multiple comparisons?Many thanks in advance,Susan McLaughlinDoctoral CandidateSPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)Dept. of Speech and Hearing SciencesUniversity of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] recon-all
Hi Freesurfer experts, We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject’s surface and mapping functional data processed in FSL’s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions. Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers), it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this? How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs? Thank you, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
