Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

To freesurfer
by Kanokwanwijit Wongsook 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer My name is nan from Thailand and I’m interest in Freesurfer software but I can’t learn from the begin by myself. I’m confused. so please, can you ad rise me in the begin point of this Freesurfer or some course to learn.Thankyou Sincerely yours,

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List of vertices in defined region
by Sarah Lavelle 05 Mar '23

05 Mar '23

External Email - Use Caution Hi there, I want to get a list of all vertex numbers within a defined region. For example, to see what vertices are in the superior frontal lobe using the DKAtlas. Would you have any suggestions? I am currently using Matlab to analyse the cortical surface mesh so it would be great to have this list in a Matlab environment. Thank you very much, Sarah Lavelle

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Re: [Freesurfer] Request for Consent to Use Derivative Work for Commercial Use
by Douglas N. Greve 03 Mar '23

03 Mar '23

Hi Zuha, I'm not the person who can give permission. I think the license allows you to use the software in the way that you are describing. I'm cc'ing Heonick Ha, one of the MGH licensing lawyers, who should be able to tell you definitively. best doug On 3/3/2023 3:30 AM, Zuha Junaidi wrote: > > External Email - Use Caution > > Dear Sir/Madam, > > I am Zuha Junaidi, writing to you on behalf of the legal team > atBrainSightAI, > <https://secure-web.cisco.com/1fenN2fK-sZMU_yj5Vozshm1nAWqMTjXfYE64fp8_qeSeG…>to > request your consent to use the Freesurfer license for commercial use. > At BrainSightAI, a connectome-based analysis startup based out of > India, we enable personalized brain mapping which has implications > across neurosurgery, neurology, and psychiatry. > > Our product involves robust pre-processing of structural MRI > modalities, and we have found that Freesurfer's mri_convert and > mri_normalize functions give us the best results. We would like to > incorporate intensity normalisation functionality as part of our > pre-processing pipeline. > > As we are conducting clinical studies to validate our product and > obtain FDA approval prior to commercialization, we need your > permission to use Freesurfer's license to access and utilize its > mri_convert and mri_normalize functions in our analysis pipeline. > > We want to clarify that we would only be using the mri_convert and > mri_normalize functions from Freesurfer's software package, and we > will comply with all the license terms and conditions while using it. > Whenever applicable, we will give proper attribution to the authors > and developers of the software in any publications or presentations > resulting from our work. > > We will strictly adhere to all the terms and conditions set forth in > the Software License. Our use of the Software will be limited to the > specific functions of mri_convert and mri_normalize. We will preserve > and maintain all applicable attributions, copyright notices and > licenses included in or applicable to the Software. Any modified > versions of the Software will be clearly identified and marked as > such, and we will not misrepresent them as being the original Software. > > We believe that incorporating Freesurfer's functions in our processing > pipeline will enhance the accuracy and efficiency of our analysis, and > we hope that you will grant us permission to use them. > > Please let us know the process to receive permission. > > Thank you for your time and consideration. We look forward to hearing > from you soon. > > Sincerely, > > Zuha Junaidi > > +91-9205209836 >

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more detailed instructions for cloning voxels & confirmation that the cloning worked
by Harriott, Emily M 03 Mar '23

03 Mar '23

External Email - Use Caution Dear FS experts, I hope this email finds you all doing well. I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me. 1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)? * I read through https://secure-web.cisco.com/1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5y… but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google. 2. How do you tell if it worked? I saw https://secure-web.cisco.com/1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmn… this previous post but it does not seem to have been answered. Any assistance would be greatly appreciated. Thank you so much! All the best, Emily Harriott PhD student, Vanderbilt University

2 2

ova.7z file unlock password request
by Anthony Maina 02 Mar '23

02 Mar '23

External Email - Use Caution Dear freesurfer, Kindly send me the 7z file unlock password Thank you

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Re: [Freesurfer] MSM error
by Glasser, Matt 02 Mar '23

02 Mar '23

External Email - Use Caution This seems a better question for the HCP-Users (hcp-users(a)humanconnectome.org<mailto:hcp-users@humanconnectome.org>) list than the FreeSurfer list, given that you are using the HCP Pipelines and MSM is an FSL rather than a FreeSurfer tool. When you repost on the HCP-Users list, you should probably note how you are calling the PostFreeSurfer pipeline. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mark Wagshul <mark.wagshul(a)einsteinmed.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, March 2, 2023 at 9:15 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] MSM error External Email - Use Caution Dear Freesurfer experts, Hi. I am running “msm” within a singularity package of the HCP pipeline (“PostFreesurfer”), and running into a strange error. Note – I have processed 15 subjects successfully without running into this error, it’s only occurring for one subject. Here is the msm call it’s failing on: /public/apps/fsl/6.0.5_cpu/bin/msm --conf=/gs/gsfs0/users/mrrc-all/PROJECTS/P65-ALL/SCRIPTS/HCP//MSMConfig/MSMSulcStrainFinalconf --inmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sphere.rot.native.surf.gii --refmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A013.L.sphere.164k_fs_LR.surf.gii --indata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sulc.native.shape.gii --refdata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A000.L.refsulc.164k_fs_LR.shape.gii --out=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L. –verbose And the error it reports is: terminate called after throwing an instance of 'std::runtime_error' what(): Cannot create directory BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L.logdir++++++++++++++++++++ Write permissions in that folder are fine, so I’m not sure what this is coming from. I’m also puzzled that it is trying to create a directory with so many “+” signs, there are no currect L.logdir folders in there. Thank you in advance for any thoughts on how to debug this. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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MSM error
by Mark Wagshul 02 Mar '23

02 Mar '23

External Email - Use Caution Dear Freesurfer experts, Hi. I am running "msm" within a singularity package of the HCP pipeline ("PostFreesurfer"), and running into a strange error. Note - I have processed 15 subjects successfully without running into this error, it's only occurring for one subject. Here is the msm call it's failing on: /public/apps/fsl/6.0.5_cpu/bin/msm --conf=/gs/gsfs0/users/mrrc-all/PROJECTS/P65-ALL/SCRIPTS/HCP//MSMConfig/MSMSulcStrainFinalconf --inmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sphere.rot.native.surf.gii --refmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A013.L.sphere.164k_fs_LR.surf.gii --indata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sulc.native.shape.gii --refdata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A000.L.refsulc.164k_fs_LR.shape.gii --out=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L. -verbose And the error it reports is: terminate called after throwing an instance of 'std::runtime_error' what(): Cannot create directory BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L.logdir++++++++++++++++++++ Write permissions in that folder are fine, so I'm not sure what this is coming from. I'm also puzzled that it is trying to create a directory with so many "+" signs, there are no currect L.logdir folders in there. Thank you in advance for any thoughts on how to debug this. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

1 0

Password for the FreeSurferVM
by Johannes.Luibl＠web.de 01 Mar '23

01 Mar '23

1 0

Neuroimaging postdoctoral fellowship at Stanford University, USA
by Mira Michelle Raman 27 Feb '23

27 Feb '23

External Email - Use Caution Dear FreeSurfer community, The Brain Imaging, Development, and Genetics (BRIDGE) lab, part of Stanford University’s Division of Brain Sciences, is seeking two full-time Postdoctoral Fellows in brain imaging and/or human genetic modeling. Ideal candidates will have a solid neuroscience, neuroimaging, and/or human genetics background. BRIDGE focuses on neuropsychiatric disorders, specifically those associated with RASopathies, such as Noonan syndrome and neurofibromatosis 1 (NF1). In our NIH-funded research, we employ three unique approaches: 1. Taking a genetics-first approach, we study children with known genetic conditions who exhibit attention problems, irritability, and deficits in social cognition. The approach differs from traditional research, which begins with the child's symptoms. 2. We apply in-depth phenotyping of the child's brain, genes, and behavior using brain imaging, genetic testing, and behavioral assessment. 3. We use large publicly available data sets (>10K children) focusing on child brain and behavioral development. Our goal is, therefore, to uncover how genetic variation and its associated downstream pathways affect children's developmental disorders. If interested, please see the official posting for additional details at https://secure-web.cisco.com/1KzHM6M8eHNAqniwUwClGLco44e39zsXfqSw4bO6Ms6b1q… Thank you, Mira Raman, Research Data Analyst BRIDGE, Stanford University

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Consequences of using -notal-check / using a poor talairach transformation
by Tyler Ward 27 Feb '23

27 Feb '23

External Email - Use Caution Hi Freesurfer developers, I am processing several thousand MRIs through Freesurfer and have come across >200 cases where recon-all failed due to the automated talairach QA check. In these cases, I do see some which have bad transformations and others which look acceptable to me. After freesurfer runs, we review the cortical ribbon from the aparc+aseg file to the quality of the parcellation. My question: what problems might arise from using the "-notal-check" on all our freesurfer runs which would not be caught by looking at the parcellation? I am also wondering if you have the "RLB700_preprocessing_statistics.pdf" document which the code references > # now run Avi's QA check on the results found in talairach_avi.log > # see document RLB700_preprocessing_statistics.pdf for details > Thanks for your time, Tyler

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Freesurfer