Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

mammillary bodies
by Jacobs H (NP) 11 Sep '17

11 Sep '17

Hello all! I am looking for a automatic or semi-automatic segmentation tool for the mammillary bodies. Any suggestions? Many thanks! Heidi

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Longitunal analysis with FS-FAST
by stdp82＠virgilio.it 11 Sep '17

11 Sep '17

Hi list,I would like to perform longitudinal analysis with FS-FAST, fMRI data.Please could you list, in summary, the processes that I should done?ThanksRegardsStefano

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Cortical thickness
by Esteban, Eva(GE Healthcare) 11 Sep '17

11 Sep '17

Hello everyone, I am trying to compare the difference in cortical thickness between two subjects by overlaying the surfaces (lh.thickness and r rh.thickness) but -diff doesn't seem to be doing the work. Does anyone know of any other commands which could be useful for this? Thank you! Eva

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Transfer files from Windows
by Fereshte 10 Sep '17

10 Sep '17

Dear FreeSurfer experts I've tried using FreeSurfer on windows with VirtualBox. I need to transfer some files on my windows to use in FreeSurfer. I've seen the same question in the frum but not appropriate answer and i couldn't find any helpful instructions on net either. I'd appreciate your help with it. Regards

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PETsurf non linear registration
by Victor Montal Blancafort 08 Sep '17

08 Sep '17

Dear Freesurfer experts, I have been working with the PETsurf pipeline. I was wondering if there is any chance to use a non-linear registration (i.e ANTS) in order to compute the %tissue per voxel in native space. Currently, I am using your pipeline to process DWI data. Due to some EPI artifacts during the acquisition, I would like to use a deformation algorithm to get rid off those artifacts that would generate false values when projecting to surface (i.e misalignment between DTI and T1 in (shrinked) frontal areas, will cause erroneous (outliers) values. If this is not possible, could you please explain in detail how the mri_gtmpvc algorithm works to compute the % tissue fraction of each voxel (to implement it)? Correct me if I'm wrong: 1) Downsample the DWI to a 3x3x3 grip (any command for that)? 2) Normalize to the high-res MRI. 3) Using the aparc+aseg?, compute the % of each ROI in that voxel (again, command?). 4) Assign in the native space, the % of ROI at each voxel. 5) Compute the tissue prob as the sum of all ROIs for a certain tissue type in that voxel. BONUS: mri_vol2surf doesn't allow either non-linear registration? Any insight will be really appreciate!! Victor Montal

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LME model and contrast
by Donatas Sederevicius 08 Sep '17

08 Sep '17

Dear freesurfer team, I’m trying to use freesurfer LME tools to check whether baseline BMI scores (BMI scores at the first timepoint) have a statistically significant effect/impact on longitudinal thickness changes accounting for baseline age and gender. The model I’m thinking of is: Y_ij = b0 + b1 * t_ij + b2 * bslBMI_i + b3 * bslBMI_i * t_ij + b4 * gender_i + b5 * bslAge_i and the contrast CM.M = [0 0 0 1 0 0]. Is this a correct way of doing it or did I misinterpret something? Thank you. -Donatas

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patch for ribbon mgz failure
by Maria Gloria Rossetti 08 Sep '17

08 Sep '17

Hi freesurfer team, I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use. Any advice? Thanks! Gloria

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答复: ROI
by Jin Bo 07 Sep '17

07 Sep '17

Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI can not display on surface(tksurfer patient lh inflated -overlay patient/label/fcd.label ). The terminal showed the following sentence: label stat field identically zero - setting to 1 However, it works well on 3T MRI. Thanks, Bo ________________________________ 发件人: Jin Bo 发送时间: 2017年9月6日 8:11:40 收件人: freesurfer(a)nmr.mgh.harvard.edu 主题: ROI Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI can not display on surface(tksurfer patient lh inflated -overlay patient/label/fcd.label ). The terminal showed the following sentence: label stat field identically zero - setting to 1 However, it works well on 3T MRI. Thanks, Bo

2 2

combining a stroke lesion label with aseg.presurf.mgz
by miracle ozzoude 07 Sep '17

07 Sep '17

Hello FreeSurfer expert, I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all -autorecon2-noaseg -autorecon3. I have done the first part: 1) mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii stroke.mgz (use freeview to check the accuracy) I want to combine the stroke.mgz with the aseg.presurf.mgz in order to create a new ROI. what command should I use to accomplish this? Thanks Best, Paul

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Why does nii2mnc fail with a neck-cropped-structural Image?
by Usman Ayub 07 Sep '17

07 Sep '17

Hi Freesurfer People, The aim is get ROI masks for my functional images and to achieve that for each of the subjects in my data, I am: 1. Running freesurfer for segmentation of structural scan, 2. Running feat analysis that would give me transformation matrices including structural2functional and then, 3. I am transforming my masks from step 1 to functional space using flirt. The first step requires me to use the actual structural image and the second step won't produce good results if I don't do brain extraction on the structural image. Now the problem is, for structural image of one of the subjects, I cannot get good brain extraction unless I use fslroi to crop the neck out first. And if I do that, the transformation matrices that I get using resulting bet image won't be usable with the freesurfer masks that I have obtained using the uncropped structural image. And if I try to use fslroi-cropped-structural-image with freesurfer, the nii2mnc command would produce this error: $ nii2mnc output_better.nii.gz > ** ERROR: nifti_image_read(output_better.nii.gz): bad dim[0] > Segmentation fault (core dumped) > I don't know how am I supposed to fix this issue. Thanks, Usman Ayub Sh

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Freesurfer September 2017