Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Hippocampal subfields questions
by Steve Petersen 24 Oct '20

24 Oct '20

External Email - Use Caution Dear Eugenio, Just two simple questions about hippocampal subfields: Q1. The volume of each hippocampal subfield is exported in mm3? Q2. I would like to compare hippocampal subfields volume measures between three groups by including the eTIV as covariate. Can I perform this group analysis by using the command line (with mri_glmfit command as for the thickness for example)?. In that case should I include some specific argument to consider in the analysis the hippocampal subfield stats of each subject?. Thank you in advance. Best, Steve

2 1

how to set Freeview Window and level values using command line
by Frank Robert 24 Oct '20

24 Oct '20

External Email - Use Caution Hello FreeSurfer Team How can I set the Freeview Window and level values using command line? In example, we can set colormap using command line. But how can I set window and level using command line rather than GUI slide bar. Thanks Frank freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2

2 1

Freesurfer crashes on mac OS
by Shirin Vafaee 24 Oct '20

24 Oct '20

External Email - Use Caution freesurfer(a)nmr.mgh.harvard.edu

1 0

To post to freesurfer list (from email)
by Shirin Vafaee 24 Oct '20

24 Oct '20

External Email - Use Caution shirinvafaee(a)gmail.com

1 0

hippocampus mesh creation from aseg.mgz
by Gonzalo Rojas Costa 23 Oct '20

23 Oct '20

External Email - Use Caution Hi: Which is the best library or software to create the hippocampus mesh using aseg.mgz segmentation file? Sincerely Gonzalo Rojas Costa

1 0

(no subject)
by saman fouladi 23 Oct '20

23 Oct '20

External Email - Use Caution hi I was running several putty windows for recond-all MRI pictures. Some putty were inactived during running. How can I activate them?

2 2

Help to create flattened images of a whole hemisphere
by Ornaith O Reilly 23 Oct '20

23 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined in Image 1. 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created and image 3 shows the error that I get when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result). 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten : mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I got the output: Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d using write iterations = 10 reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% of total) reading original vertex positions... minimizing metric distortion induced by projection... MRISunfold() max_passes = 1 ------- tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 12 niterations 40 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 -------------------- /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards

3 3

pial reconstruction with flairSPACE flag
by Octavian Lie 23 Oct '20

23 Oct '20

External Email - Use Caution Dear All, I have downloaded the latest stable (7.1.1), and ran recon-all with and without a high-quality FLAIR SPACE sequence (per Andre's protocols). I noted a new behavior compared with previous FS versions: using the FLAIR makes the pial reconstruction more conservative (blue contour in attached), looks eroded compared with the run without (red contour), the latter which follows the pial anatomy closer (still, it needs some editing out dura at times). I am not sure why that is, I am not sure it is registration per se (the blue pial surface is burrowed within the red one on all sides). Please advise, is there a way to 'relax' the recons with FLAIR SPACE to overlap better with the actual pial surface? Thank you, Octavian

1 0

Help to create flattened images of a whole hemisphere
by Ornaith O Reilly 23 Oct '20

23 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined below: Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ tksurferfv bert lh inflated freeview -f /Applications/freesurfer/7.1.1/subjects/bert/surf/lh.inflated:curvature=/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.curv -viewport 3d /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created but when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result) a pop up appeared saying "please move cursor to a valid vertex". 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten : mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I got the output: Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d using write iterations = 10 reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% of total) reading original vertex positions... minimizing metric distortion induced by projection... MRISunfold() max_passes = 1 ------- tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 12 niterations 40 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 -------------------- /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards Ornaith O'Reilly

2 1

please help me
by saman fouladi 23 Oct '20

23 Oct '20

External Email - Use Caution hi How long does it take to execute a recon-all command? and what message indicates that it finished? Is there a way to speed it up? thank you

2 1

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