Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

control.dat not working
by Rosalia Dacosta Aguayo 05 May '23

05 May '23

External Email - Use Caution Dear Freesurfer subjects, After saving my control.dat file into the tmp folder and running the command line recon-all -autorecon2-cp -autorecon3 -s.... It does not seem to parse the control.dat file correctly and find the control points. This is what I get (in recon-all.log): #@# Intensity Normalization2 Fri 5 May 08:01:43 CEST 2023 /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/mri mri_normalize -seed 1234 -f /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz /bin/tcsh: /home/rosalia/software/fsl/fslpython/lib/libtinfo.so.6: no version information available (required by /bin/tcsh) setting seed for random number genererator to 1234 using control points from file /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 0 control points... Doing gentle normalization with control points/label error: No such file or directory error: MRI3dGentleNormalize: mean = 0.0, nctrl = 0, norm failed Interestingly, when I saved the control points, freeview offered saving it as control.json, and the content of control.dat is, indeed, follows the JSON format. I renamed the file to control.dat (as in the tutorial). Is it possible that I should have kept it as control.json? P.S.: There is also a typo in the log. "random number genererator" should be "random number generator". :) Kind regards, Rosalia

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freeview rh and lh overlay_mask files both showing in the lh hemisphere
by Jewelia Karina Yao 05 May '23

05 May '23

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to use freeview to load the rh and lh inflated surfaces together with overlays and overlay masks. I'm able to this separately and successfully for each hemisphere, but when I try to load the hemispheres together, both of the overlay_mask files show up on the left hemisphere and not the right hemisphere. The following is the command I'm using: freeview -f ${SUBJECTS_DIR}/${SUBJECT}/surf/rh.inflated:curvature_method=binary:overlay=rh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/rh.ve_20pct.thresh.label \ -f ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.inflated:curvature_method=binary:overlay=lh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/lh.ve_20pct.thresh.label I've tried running this with 7.1.1 and 7.2.0 on Mac 10.15.7 and Linux w/Ubuntu 22.04 but still run into the same issue. Let me know if there's something I'm missing or if there's a better way to troubleshoot. Thanks! Jewelia

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Why is this happening?
by Rosalia Dacosta Aguayo 05 May '23

05 May '23

External Email - Use Caution Dear Freesurfer's experts, Why is this happening? Kind regards, Rosie

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mris_flatten .flat output in matlab
by Manenti, Giorgio 04 May '23

04 May '23

External Email - Use Caution Dear Experts, My aim is to get circular ROIs. At the moment i am trying it on the flatmap, and i am writing a matlab script to do the task. However, I am getting a problem to open the output file (.flat) of the mris_flatten function as surface in MatLab. I obtain the patch as "mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat “. The output is working properly on Freeview. However to make the circular ROIs pipeline faster and robust I would like to use Matlab. I tried to open the flattened patch via “read_curv”, “read_surf”,”read_patch” and also “MRIread” but all are returning the error “ could not open file ….” . (i) Is there any suggestion to solve this issue? I would like to open the patch as i would do for a mask and afterwards create a circular ROI per each area of interest given the functional clusters (from sig.nii file) projected on the flatmap. (ii) Is there any alternative to get circular ROIs on surface? Perhaps without GUI? For example via ‘mris_pmake’ ? Would i still require a flattened surface right? Many thanks in advance Best Giorgio

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apply an existing linear transform to a GRE phase map
by Balentine, Daniel Grimm 04 May '23

04 May '23

External Email - Use Caution Hello FreeSurfer Developers, I hope you are well. I'm attempting to apply an .lta file generated by mri_robust register. The files I want to apply the transform on are GRE phase maps, so I don't want to do any resampling. I was looking around mri_vol2vol, but all the examples seem to involve resampling to a target scan. How would I go about this if I simple want to apply this linear transform on the phase maps (nii) in freesurfer? 1. Freesurfer version 7.3.0 2. Platform: CentOS Version 7 Sincerely, Daniel Balentine Data Analyst Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 - 13th Street Charlestown, MA 02129 dbalentine(a)mgh.harvard.edu

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Is it possible to edit this kind of error with cp?
by Rosalia Dacosta Aguayo 04 May '23

04 May '23

External Email - Use Caution Dear Freesurfer's experts, Is it possible to correct this kind of error with cp? Thank you, Rosalia

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Virtualbox unzip password
by neda afzalian 04 May '23

04 May '23

External Email - Use Caution To whom it may concern > Would you please send me the password for unzipping the virtual box file? Best Neda

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change ants N4 bias field correction parameter in recon-all pipeline
by 刘梦醒 04 May '23

04 May '23

External Email - Use Caution Hello FreeSurfer Developers, Some T1s we collected have higher intensity in the occipital cortex. The default recon-all failed skull stripping and wm/gm segmentation in that part of the brain. After several tests, we found that doing ants N4 bias field correction with a shrink factor of 1 could fix the problem in most cases. We are aware that the same correction is included in recon-all, while with default parameters. We wonder if there is one way to specify the parameter for the bias correction in recon-all? If not, what would you recommend in this situation? A bias correction before recon-all, and still do another correction inside recon-all? The freesurfer we use is 7.1.1. Thanks! best, Mengxing

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Request for Password for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Payam Jannatdoust 03 May '23

03 May '23

External Email - Use Caution Dear FreeSurfer Support team, My name is Payam Jannatdoust and I am a medical student and neuroscience researcher affiliated with Tehran University of Medical Sciences. I am writing to request the password for the file named "FS_7_2_0_Ubuntu_18_04_06.ova.7z". This compressed archive contains the virtual machine image of Ubuntu with Freesurfer installed on it. As a part of my research work, I need to use Freesurfer for the analysis of neuroimaging data. However, due to the unavailability of appropriate resources, it has been difficult for me to install and configure Freesurfer on my computer. I came across the virtual machine image of Ubuntu with Freesurfer installed, which I believe would be a great resource for my research. I would be grateful if you could provide me with the password for the file "FS_7_2_0_Ubuntu_18_04_06.ova.7z" so that I can access the virtual machine image and start my research work. Thank you for your assistance in this matter. I look forward to hearing from you soon. Sincerely, Payam Jannatdoust

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contrast-FSGD question
by Fred d'Oleire Uquillas 03 May '23

03 May '23

External Email - Use Caution Dear Fs support, If I have the following FSGD with 4 classes and 3 variables, and I'd like to run an interaction of ROIa x ROIb controlling for the third covariate (eTIV), would I use the following contrast? [0 0 0 0 0.25 -0.25 -0.25 0.25 0.25 -0.25 -0.25 0.25 0 0 0 0] For the interaction of ROIa x ROIb x class + eTIV. Thank you so much in advance for your help! All the best, Fred

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Freesurfer May 2023