Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Three qdec analyses, different results
by Wang, Lily 14 Feb '20

14 Feb '20

Hi Freesurfer Team, I made a qdec table with columns fsid, disease status (control and diseased), age, df, db, dtotal (which are three continuous psychological test scores). I performed one analysis in qdec with disease status as the discrete factor and each of the three test scores as the continuous factor with no nuisance factor chosen, for a total of three analyses. All three analyses ran successfully but when I choose "Does the average thickness differ between Control and Diseased?", which should ignore the test scores (right?), and applied an FDR = 0.05, I get wildly different results among the three analyses even though I believe I should get the same results since it is the same pool of subjects in all three analyses. Did I do something wrong? Thank you, Lily

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Conversion between lta file type
by Christian O'Reilly, Dr 14 Feb '20

14 Feb '20

External Email - Use Caution Hi, How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1 (LINEAR_RAS_TO_RAS)? Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn z.nii.gz as the original volume x.nii.gz transformed according to y.lta? I tried with mri_vol2vol but somehow I could not figure a way to make it work properly. Also, given a volume containing a full head and a second volume containing a stripped skull, what is the best approach with FreeSurfer to transform the brain so that it is properly registered with the full head (using an affine transform)? I tried many different ways to get it done with mri_robust_register and also with bbregister, but somehow I could not get a satisfactory result (i.e., I could always get a much better fit by hand using freeview).... Thank you! Christian

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Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 14 Feb '20

14 Feb '20

External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from mri_gtmpvc, Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale (reference regions) for SUVR in PET space. What do you prefer or recommend? 2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii --regheader because rbv.nii.gz is in different space. but when overlaid with them, registration is not correct. (WHY) rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space) I just wanted to use the pv-corrected image for image processing. and you also said, smoothing is required after PVC. (Surface or volume based smoothing (resonable). Best regards, Soo

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mri_glmfit-sim error
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Hi there, I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with -perm-force” Please let me know how to process mri_glmfit-sim. Thank you, Gwang-Won

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Cluster-wise correction for multiple comparisons
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Hi there, First, I ran "mri_glmfit" using mask including 4 ROIs(file name: 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable 4_ROI.label --surface fsaverage lh - --fwhm 5 -eres-save. Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons. Please let me know how to process "mri_glmfit-sim" using masks (file name: 4_ROI.label) . Is it right? “mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs --2spaces --bg 1” Thank you, Gwang-Won

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New release plans?
by Dan Fitch 14 Feb '20

14 Feb '20

External Email - Use Caution Hi folks! I checked the wiki and github, but couldn't find anything about milestones or plans for the next major release of Freesurfer. Are there any loose dates or targets? (We're near the start of a 5-year imaging study, and trying to plan for training and pipeline changes...) Thanks for any hints you can drop! Dan Fitch Research Software Engineer University of Wisconsin-Madison Center for Healthy Minds

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CorticalParcellation for mask
by sang ho shin 14 Feb '20

14 Feb '20

External Email - Use Caution Dear freesurfer experts, I am trying to make mask for '1027 ctx-lh-rostralmiddlefrontal, 2027 ctx-rh-rostralmiddlefrontal ' on MNI standard image (MNI152_T1_2mm_brain.nii) (FreeSurferColorLUT <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurf…> ) I can get the mask of native participant's image after completing 'recon-all' (mri_binarize --i nor86_ahj_fs/mri/aparc+aseg.mgz --match 1027 --o nor86_ahj_dlpfc/nor86_ahj_rostalmiddlefrontal.nii.gz) But I now want to get the mask on MNI standard image, not native image. I wonder if you can help me. Best regards, Sangho ᐧ

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uploading PALS12 + overlay
by Barletta, Valeria 14 Feb '20

14 Feb '20

Dear Freesurfers, Is there a way to visualized the PALS12 atlas in the same view with this overlay (attachments) on tksurfer or freeview? Thanks, Valeria

2 1

Troubles using optseq
by FRILEUX Solene 14 Feb '20

14 Feb '20

External Email - Use Caution Good morning, I am writing to you in order to ask you some help about optseq. I am struggling using the command cmx . I need to save the paradigms as matlab files (90 paradigms) However, the terminal tells me it is not able to find this function. Optseq id is $Id: optseq2.c,v 2.22 2011/04/21 19:48:51 greve Exp $ Computer is iMac retina 5K 27 pouces, 2019. 3 .1GHz Intel Core Here is the text terminal send me : /Applications/freesurfer/bin/optseq2 \ > --ntp 720 --tr 1.25 \ > --psdwin 0 16.25 \ > --ev foodCHoice1 3.5 25 \ > --ev foodCHoice2 3.5 25 \ > --ev foodCHoice3 3.5 25 \ > --ev foodCHoice4 3.5 25 \ > --tnullmin 4\ > --nkeep 90 \ > --o subcontrolfood \ > --mtx firdesign -bash: --mtx: command not found Thanks a lot, Solène Frileux

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Mismatch between glmfit results and mris_anatomical data in one hemisphere
by Hooren, Roy van (Alumni) 14 Feb '20

14 Feb '20

External Email - Use Caution Dear FreeSurfer experts, In FreeSurfer (Darwin-OSX-stable-v6-beta-20151015 build, operating on Yosemite 10.10.5) I’m running into an issue that I would like to request your expertise on. The procedure I used: I have a dataset of 77 participants, which have been processed through the standard recon-all and qcache pipeline. Subsequently I’ve used mris_preproc to prepare the data for group anaylysis, using FSGD files with the DeMeanFlag 1 and ReScaleFlag 1 options. After that, MRI_glmfit was run with the appropriate contrasts. Finally, mri_glmfit-sim was used to apply cluster correction. The only (minor?) issue until this point is that mri_glmfit-sim often runs into a “Segmentation fault” error, which can be bypassed by simply rerunning mri_glmfit-sim until it does work. Having done this, there seem to be no further issues and the clusters resulting from the glm analysis, also after cluster correction, look nice in both hemispheres. To further interpret the resulting clusters, I extracted individual labels from the annotation files resulting from the glm analyses, using mri_annotation2label. These labels were checked and looked correct. Next, these fsaverage-based labels were then warped back to the individual level, using mri_label2label, with each subject as the –trgsubject. The registration between individual labels and their respective inflated brain was checked and looked good on every hemisphere. At this point mris_anatomical_stats was used to extract average cortical thickness data for each cluster in each participant. Finally, using aparcstats2table, these values were placed in a table to be imported in R statistics software for visualization purposes. What the main problem is: The main issue I would like to ask your advice on appeared when the data was analyzed in R. In R, the same regression models were reconstructed as the ones that were used in mri-glmfit, in order to parse and visualize the contribution of each predictor in the model to the cortical thickness measure in each cluster. In the right hemisphere, the results were as expected for every cluster, showing highly significant effects of the variables of interest (p<0.001). However, when the same was repeated for the clusters in the left hemisphere, none of the expected effects were seen, with p values easily rising above 0.90. As the clusters in the left hemisphere survived mri_glmfit-sim cluster correction, and the outcome measure is average cortical thickness extracted from these clusters, there should be no way that this is correct data. The fact that the data looks incorrect specifically in the left hemisphere, while they are as expected for the right hemisphere, leads me to believe left and right hemisphere may have been mixed up in one of the scripts. However, I have checked the used scripts meticulously for any point at which left and right hemisphere may have accidentally been mixed up, but after repeated checks I have not found any issues. The procedures from mri_label2label and onwards were also repeated with separate scripts for left and right hemispheres as a sanity check, and the resulting thickness values did not change. As mentioned before, the label overlays look good for both hemispheres at the individual level, so I do not believe anything went wrong at this point. I would like to ask if you have any suggestions as to where you suspect the problem might lie and would greatly appreciate any pointers you might have. If any more information is needed, please let me know. Kindest regards, Roy

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