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30132 discussions

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

2 5

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

1 0

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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ERROR: nu_correct
by Graduate Imaging 12 Feb '20

12 Feb '20

External Email - Use Caution Hi, I've been processing some 3T MRI scans through Freesurfer and recently implemented the use of the -3T flag for nu-correction. I have processed about 200 scans and the majority of them have gone through with out an issue. However there are a handful that I received and error: nu_correct message in the recon-all log. I've visually inspected these images and there appears to be nothing wrong with them. I've attached the error code below. Does anyone know what might be causing this? Furthermore, one of these images had actually been processed without a 3T flag prior without issues so it appears to be intrinsic to flag. Assertion failed: (pxp->bf_refcount <= 0), function ncio_px_sync, file ./posixio.c, line 798. nu_evaluate: crashed while running minc_modify_header (termination status=6) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct

1 0

Hippocampal segmentations -- how to make manual adjustments
by Kathy Reding 12 Feb '20

12 Feb '20

External Email - Use Caution I would like to manually adjust the hippocampal segmentations created by the hippocampal/amygdala sub-field segmentation pipeline. The hippocampal head boundary with the amygdala was poorly defined in my subjects (1mm isotropic images), and I would like to manually adjust this boundary. 1) I used the longitudinal pipeline (subjects had three visits each). Ideally, I would like to do this once per subject (i.e., on the subject average), but am not sure if that is possible, or if the subject average boundaries would maintain their accuracy once applied to each individual visit. If this is not possible, I would like to adjust only a single image per subject/visit (outline of the whole hippocampus) and apply it to two of to the three available segmentation (HBT, CA), or more importantly, extract the volumes in a similar manner to the FS provided sub-field output. 2) I would like to know how the alveus is assigned in the CA and HBT segmentations. It appears to be included in the hippocampus in my images, and I am curious if this is an error. Should it be excluded? Best, Kathy Reding

1 0

Recon-all autorecon2 exited with error
by Benjamin Ineichen 12 Feb '20

12 Feb '20

External Email - Use Caution Dear Freesurfer experts, I edited the brainmask.mgz to erase some dura which caused problems with the pial surface in a subject. I then re-ran recon-all using: recon-all -qcache -s test1_edit -autorecon2 However, the recon-all finished with errors. Attached the log and error files. What is the problem? Thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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