Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Question about scaling intensities
by Hye Min Shin 13 Dec '20

13 Dec '20

External Email - Use Caution Hello, I was wondering if there was a way to scale intensities of normalized T1 images. For instance, I wanted to rescale intensities of white matter from [0,110] to [-1, 1] and intensities gray matter from [0, 80] to [-1, 1]. I wanted to rescale intensities to get consistent normalization levels across all T1 images for neural networks. Best, Julia Shin

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Computing thickness from woT2.pial surfaces
by Antonín Škoch 13 Dec '20

13 Dec '20

External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

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Does segmentation depend on input orientation {Disarmed}
by Nederpelt, D. van (David) 13 Dec '20

13 Dec '20

External Email - Use Caution Hi, I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and once on this image converted to LAS orientation I would expect the output (especially in volume) to be equal, because freesurfer reconverts it to its own orientation if I understood correctly. However, I found that the segmentation and output volumes differed depending on the input orientation. So while in fact both images are actually the same, the output differs. What would be the reason for this difference in output? Any help would be much appreciated Kind regards, [cid:image002.png@01D40E30.3E299A80] David van Nederpelt, MSc. | PhD Candidate Radiology and Nuclear Medicine Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands E: d.vannederpelt(a)amsterdamumc.nl<mailto:d.vannederpelt@amsterdamumc.nl> http://secure-web.cisco.com/1yrDXcY3eqFuC9AUoZEDMJuZ0ojaLvbgGcFJ6eX6d_5r-mV…<http://secure-web.cisco.com/19L5zWn8iSh3B8KxDO60RgDjt3gGMMF3QPQVn6IQE8toN2A…> | http://secure-web.cisco.com/1yZ-GMAcIXR2JVaYlHW4MkWh3pH3uqqnFtkndplOESePIIi…<http://secure-web.cisco.com/1iEODCCa6CXtMd9bQZjIQntIRXNo8vPN3sVVSIFZ5bZfflE…> / http://secure-web.cisco.com/1WysKpLXmYNNaIkdkI_HIp4gMvxMuUUMRBYKfxhbUgZoyKo…<http://secure-web.cisco.com/1AZmq9gaNj_RNBv07qct3dKWqN9IDFqy7xUHiAIz_0p7qYt…> ______________________________________________________ ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/1Ai9BHY5QjRrNjsey9Ku_Ls90P8m7yD1J3X1ZEtstl9pbp9… AMC disclaimer : http://secure-web.cisco.com/1SIW7YiOGJ67yQ9iSniK8HIFxe7Ww4tUic1RZXHUlvGbSzN…

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question about PVC of PETSurfer
by 蒋袁芳 13 Dec '20

13 Dec '20

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough, it made the SUVr of hippocampal subfield we get is not accurate. So we want to use the PVC function of PETSurfer. Whether the PETsurfer output the result of PET image after PVC ? so that we can use it directly to registering with MRI image. If it doesn't output the result, can we save it in some ways? Thank you for your guidance.

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Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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inflated surface with holes
by Jie Zhao 13 Dec '20

13 Dec '20

External Email - Use Caution Hello Freesurfer Team I have some questions about the inflated surface. As is shown in the attached pictures, there are one big hole and three small hole on the right hemisphere, one big hole on the left hemisphere. Could anyone give me some suggestions to handle it. If you need any files, please let me know. Thanks in advance! Jie Zhao

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recon-all error {Disarmed}
by Devanshi jain 13 Dec '20

13 Dec '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to convert my .nii files (taken from ADNI dataset) to subject files (like bert). For the same I'm following this website : https://secure-web.cisco.com/13_r_7kEeP_WS7SHxH0ECZXOxZuTEltmsSnlVNl81ZLfHE… I'm getting an error while performing step 4 of 'Running Freesurfer' heading. Command that is giving error : recon-all -all -subjid <subject_id> Here my <subject_id> is subject_0295 Error on the terminal : recon-all -s subject_0295 exited with ERRORS at Tue Dec 8 18:25:40 IST 2020 The freesurfer/subjects/subject_0295/scripts/recon-all.log file didn't mention any specific error. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I have attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 16.04.7 LTS 3) recon-all.log: see attached -- Regards, Ms. Devanshi Jain

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About volumetry results by Freesurfer
by fahimeh palizban 12 Dec '20

12 Dec '20

External Email - Use Caution Hello, I am a Bioinformatician using Freesurfer for Brain volumetry analysis particularly for clinical usage. I encountered an issue when using Freesurfer for a patient having MRI data at two different time points; The volumes related to some brain sites have been increased when comparing with the previous MRI data and it is kind of impossible biologically. It would be kind of you to inform me of the mentioned problem and its reason. Thanks for your time and consideration Best regards Fahimeh

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Re: [Freesurfer] Computing thickness from woT2.pial surfaces {Disarmed}
by Antonín Škoch 11 Dec '20

11 Dec '20

External Email - Use Caution Hi, Bruce, I did not find any mris_thickness command line option for masking medial wall during thickness computation. The masking of ?h.thickness file ex post would not probably help, since it is not equivalent. I tested this by running mris_anatomical_stats (which I suppose by principle takes medial wall into account) and obtained still slightly different results. So I finally retreated to rerunning recon-all -pial and recon-all -T2pial and stored ?h.thickness of both processes. Regards, Antonin You probably want to mask the medial wall Bruce On Dec 9, 2020, at 11:31 PM, Antonín Škoch <a...(a)ikem.cz> wrote: External Email - Use Caution Hi, Bruce, in the meantime, I found the old thread https://secure-web.cisco.com/1aNvaY2F2Wzk88I3TCWDZ8sNnAxHgbRgs7ryiKYBIUsjQE… which suggests to set -N 20 parameter to mris_thickness to make thickness computation consistent to mris_make_surfaces. Indeed, the values are now consistent, with exception of several thousands of vertices mainly around medial wall. Is here any other option missing, which makes mris_thickness computed values of thickness fully consistent to mris_make_surfaces? Thank you in advance, Antonin Hi, Bruce, thank you for the instructions! I ran mris_thickness on one example subject to test the procedure. However, inspecting the values of created thickness file, I encountered problem. In many locations, the values of thickness file differ from the values of thickness file created in recon-all -T2pial. Even when the input files used for thickness measurement are (should) be the same. (I double-checked my input surfaces, when I use woT2.pial surface, the thickness values are different everywhere). Attached see the binarized difference of these thickness files with the cursor, where difference is zero (red spots) and where is non-zero (transparent). Could you please clarify, where could be the problem? Does not the thickness computation in mris_make_surfaces use different options? Could it be the reason, that I am operating with data processed by longitudinal stream? (I don't think so...). This inconsistence makes me puzzled. Regards, Antonin Hi Antonín You can specify what surfaces to use in mris_thickness: mris_thickness -pial <path to pial surface> -white <path to white surface> … cheers Bruce From: freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Antonín Škoch Sent: Wednesday, December 9, 2020 6:16 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Computing thickness from woT2.pial surfaces External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0. Thank you in advance, Antonin Skoch

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Error: must specify as many DWI dicoms as subjects
by Shanika Jayakody 10 Dec '20

10 Dec '20

External Email - Use Caution Dear FreeSurfer team I have been trying to run trac-all & keep get the error " too many ('s must specify as many DWI dicoms as subjects" There is no mismatch between my subjects list (the number and IDs) and dcmlist. I have tried changing spaces after "\" too Any suggestion is appreciated- I have attached here my configurationfile Many thanks Oshad

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Freesurfer December 2020