Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

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

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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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Desikan and Killiany atlas
by Valentina Mancini 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, we used the Desikan and Killiany atlas to build individual head models in order to project surface EEG data in the inverse space. We would like to plot on the cortical surface the regions of the D&K atlas where we find a different functional activation. As I understand, there is a way to plot statistically significant results with tksurfer, but in our case we cannot show our statistical values because we should take into account also epochs and frequency and we can do that only with a time-frequency plot. Is there a simple way to get a figure of the cortical surface with a set of predetermined regions of the D&K atlas highlighted only for visualization purpose? Best regards, Valentina Mancini

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Coordinates transformation from conformed space to the original FLAIR image
by Xiaojiang Yang 13 Feb '20

13 Feb '20

External Email - Use Caution Hi everyone, I have used both T1 and (T2) Flair images as inputs to recon-all, and I have generated some coordinates (ROI) that I can transform to the original T1 images. Basically, I use the two matrixes obtained from the mri_info -- vox2ras commands: Sr = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/orig/001.mgz Sc = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/T1.mgz For a given point Coordinate=(x, y, z, 1) in the conformed space, I get the coordinates in the original T1 space using the formula: t1_Coordinate = inv(Sr) * Sc * Coordinate. The above formula works fine. But I also want to get the transformed coordinates in the Flair image space. I have used a similar way: Srf = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/orig/FLAIRraw.mgz Sc = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/T1.mgz flair_Coordinate = inv(Srf) * Sc * Coordinate. But the above calculation is not correct. Does anyone have an idea of how to get this flair coordinate? Thank you!!! Xiaojiang

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freesurfer error in matlab
by Miguel Ángel Rivas Fernández 12 Feb '20

12 Feb '20

External Email - Use Caution Dear Freesurfer devs, I am trying to run FreeSurfer in Matlab and I received the following error message dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I tried to fix this error disabling the SIP but this did not work. Maybe could be due to the gcc compiler? Any help would be appreciated Thanks in advance Best regards, -- *Miguel Ángel Rivas Fernández*

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Freesurfer February 2020