Freesurfer

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30084 discussions

Using The Buckner Cerebellum Parcellations
by Erik O'Hanlon 02 Jul '21

02 Jul '21

External Email - Use Caution Dear FS Experts, I'd like to use the Bruckner 7 Network parcellations and have downloaded the files as per the wiki link. My Freesurfer analysis on all my subjects is sub millimetre and I have conformed my data to that using the -cm in my recon_all. I can run the recon_all with the same settings for the FSL MNI 152 1mm template as described but is there a straightforward way to get the Buckner nii file to match that space? Thanks in advance for any advice Erik

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Re: [Freesurfer] SAMSEG thresholds
by Stefano Cerri 02 Jul '21

02 Jul '21

External Email - Use Caution Hi all, Just few clarifications: 1) Lesions are segmented in SAMSEG with the label 99. 2) @Paul: The script Koen was talking about is not yet in the repo (hopefully we will commit it soon) @Alberto: if you are just interested in *only* the volume of vascular lesions for different thresholds you can also run SAMSEG with the --save-posteriors flag to obtain lesion probabilities (in yourSeg/posteriors/Lesions.mgz). Then you can play with mri_binarize and mri_segstats to obtain lesion volumes for different thresholds without re-running anything. Hope it helps. Best, Stefano Hi Alberto, Koen and Stefano, You can get the behavior you want/expect by counting the number of voxels > assigned to lesions in the seg.mgz file - there is a ready tool for that in > FreeSurfer but I don't remember off the top of my head what the correct > command is (a search on the mailing list should be able to reveal it) > You should be able to do this with mri_segstats, e.g. ``` mri_segstats --seg /path/to/seg.mgz --o test.txt ``` You'll also need to know the label number in the FreeSurfer lookup table > for lesions - perhaps Stefano can tell you what it is (?) The label for lesions should be specified in `$FREESURFER_HOME/FreeSurferColorLUT.txt`, right now there seems to be 2 entries: ``` # wm lesions 498 wmsa 143 188 143 0 499 other_wmsa 255 248 220 0 ``` A few months ago Stefano Cerri wrote some code to correct this behavior > (and apply different thresholds without having to re-run everything from > scratch), but it never made it into the repository (my fault). Koen/Stefano, just to double-check my understanding, and you referring to this script that Stefano wrote? - https://secure-web.cisco.com/12C09A1Pra-JQ3_eWwPneWHlTs8QZ2h-wDRi-AlByffQ_Q… My understanding is that this could be used to update the priors of the model without having to re-run everthing. Not sure if what is being discussed here is related or something completely different. I've been working on generalizing that script to n-classes here: - https://secure-web.cisco.com/1VNfWVD_6T2AndQf1rq6BsPpYglmbJ3GzN01rptI6VZge7… -Paul _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1JpWiCtEjoGvM3-M_AnpjGHywxhvQwt3I6V2dThQ0HgMB8… Hi Alberto, In the current implementation the volume reported in the table is simply the sum of the lesion posterior probabilities, i.e., it is not affected by the threshold used to create the crisp segmentation result for the lesions. A few months ago Stefano Cerri wrote some code to correct this behavior (and apply different thresholds without having to re-run everything from scratch), but it never made it into the repository (my fault). You can get the behavior you want/expect by counting the number of voxels assigned to lesions in the seg.mgz file - there is a ready tool for that in FreeSurfer but I don't remember off the top of my head what the correct command is (a search on the mailing list should be able to reveal it) You'll also need to know the label number in the FreeSurfer lookup table for lesions - perhaps Stefano can tell you what it is (?) Koen On Thursday, July 1, 2021, Alberto Del Cerro Leon <bertocerron(a)gmail.com<mailto:bertocerron@gmail.com>> wrote: External Email - Use Caution Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am analyzing the vascular lessions aplying several thresholds. I would expect that lower thresholds results in lower volumes but dont seems like that. What is the reason?

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Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data
by Corinna Bauer 01 Jul '21

01 Jul '21

External Email - Use Caution Hi Bruce, I am just following up on this. Were you able to get mri_normalize to run on this mp2rage data? Thanks, Corinna On Wed, May 5, 2021 at 6:50 PM Corinna Bauer <corinnab83(a)gmail.com> wrote: > Great, thanks. The nu.mgz is attached. > > Corinna > > On Wed, May 5, 2021 at 6:47 PM Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> > wrote: > >> Hmmmm, if you send us the data we will take a look. Just the inputs to >> mri_normalize should do it for this case >> >> Cheers >> >> Bruce >> >> >> >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < >> freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer >> *Sent:* Wednesday, May 5, 2021 6:45 PM >> *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage >> with MP2RAGE data >> >> >> >> * External Email - Use Caution * >> >> Hi Bruce, >> >> >> >> The nu.mgz input into mri_normalize looks ok to me (screenshot attached), >> as does the talairach registration. >> >> >> >> Corinna >> >> >> >> On Wed, May 5, 2021 at 5:39 PM Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> >> wrote: >> >> Can you take a look at the volume that was the input to mri_normalize and >> see if it looks ok? And check the talairach >> >> >> >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < >> freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer >> *Sent:* Wednesday, May 5, 2021 5:25 PM >> *To:* Mailing Freesurfer List <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject:* [Freesurfer] error at 3d normalization pass 1 of 2 stage with >> MP2RAGE data >> >> >> >> * External Email - Use Caution * >> >> Hello all, >> >> >> >> I am trying to run recon-all on MP2RAGE data from Philips and it exits >> with errors at this point: >> >> 3d normalization pass 1 of 2 >> error: No such file or directory >> error: MRInormFindControlPoints: could not find enough control points >> >> error: No such file or directory >> error: MRInormFindControlPoints failed >> Command exited with non-zero status 253 >> >> >> >> The log file is attached. The input file was the MPRAGE generated on the >> scanner console (i.e. not the T1 map). I attached a screenshot of orig.mgz >> viewed in fsleyes. Any thoughts? >> >> >> >> Thanks! >> >> >> >> Corinna >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1dzAvSjb2xg057o7RyKJZrQAEUSNDKYyNvvSNj-Q1W3fj-… >> <https://secure-web.cisco.com/1QClCCeXykBScK8d5iq23hqFkPyT2qn3mpaj7VqrhnWopp…> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at *MailScanner has detected a possible >> fraud attempt from "secure-web.cisco.com" claiming to be* >> http://secure-web.cisco.com/1QIBq5EkkrXvBYedkVZBu1QSZSDY095TOl1_qa7F6M9d384… >> <http://secure-web.cisco.com/1rULMMfo2yJZfoOtKTGPpqqVNGJEBAprhcfVvdoBUoB2M0U…> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1dzAvSjb2xg057o7RyKJZrQAEUSNDKYyNvvSNj-Q1W3fj-… >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://secure-web.cisco.com/1QIBq5EkkrXvBYedkVZBu1QSZSDY095TOl1_qa7F6M9d384… . If the e-mail was >> sent to you in error but does not contain patient information, please >> contact the sender and properly dispose of the e-mail. >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> >

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SAMSEG thresholds
by Alberto Del Cerro Leon 01 Jul '21

01 Jul '21

External Email - Use Caution Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am analyzing the vascular lessions aplying several thresholds. I would expect that lower thresholds results in lower volumes but dont seems like that. What is the reason?

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NIMH Online Workshop on Naturalistic Stimuli and Individual Differences - August 2021
by Molfese, Peter (NIH/NIMH) [E] 01 Jul '21

01 Jul '21

External Email - Use Caution The Center for Multimodal Neuroimaging (CMN) is thrilled to announce the upcoming workshop on Naturalistic Stimuli and Individual Differences with a range of extramural and intramural speakers presenting cutting-edge work. The workshop seeks to (1) bring together top scientists using naturalistic stimuli and/or the study of individual differences in neuroimaging; (2) showcase theoretical, methodological, and analytical advances in these areas of research; and (3) serve as a catalyst for collaborations between presenters, biomedical NIH researchers, and experts from around the world. Due to the ongoing coronavirus pandemic, the workshop will feature virtual presentations and roundtables in a unique format open to the public. Presentations will be available to stream on-demand starting August 1, 2021. Attendees will be able to view the presentations in their own time, and submit questions to speakers through an online portal. In September, the speakers will again virtually reconvene for a round-table discussion to address some of the attendee questions as well as discuss larger questions in the field moving forward. More information and registration can be found at the link below! https://secure-web.cisco.com/1gUCi1nAb5eIIfmp-e8PHroYHwLS_30qYDB7AOQWmmytxE… Tweets/retweets appreciated: #cmnworkshop2021 -- Peter J. Molfese, Ph.D. [E] Staff Scientist, NIMH Science Lead | Center for Multimodal Neuroimaging Building 10, 1D80 10 Center Dr Bethesda, MD 20892-1148 Email: peter.molfese(a)nih.gov<mailto:peter.molfese@nih.gov> Phone: (301) 402-1350 cmn.nimh.nih.gov<https://secure-web.cisco.com/1jzRlPyc3jjA4x_0RRoeJMH7gad9a3qz5Zqykd5QphbYe8…>

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When GM segmentation is not good enough
by Rosalia Dacosta Aguayo 01 Jul '21

01 Jul '21

External Email - Use Caution Dear Freesurfer team, I was wondering if there is any way to improve GM segmentation with FreeSurfer in cases like this, when all they GM has not been included by FreeSurfer: https://secure-web.cisco.com/1Vs511OuC3LYOAyRmiyTn4sfCMK9fVD-cPX8iYOmw7fzgP… Kind regards, Rosie

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problem with mris_compute_lgi
by Bernardoni, Fabio 30 Jun '21

30 Jun '21

External Email - Use Caution Dear FS experts, when running mris_compute_lgi, the make_outer_surface step produces an error: >> reading filled volume... /bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81860215899812157.load_mgh.m.mgh for reading Looking more closer at what produces the error, it is the MRIread function: vol=MRIread('..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz') /bin/bash: /scratch/tp81861321896965219.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81861321896965219.load_mgh.m.mgh for reading ERROR: loading ..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz as MGH vol = [] I do not understand where the /scratch/tp81861321896965219.load_mgh.m.mgh is created/located. Is it within the rh.pial.filled.mgz? Even going through the MRIread function I couldn't figure out. Maybe the error is actually in the mri_fill step (that however exits with no error) Thanks in advance for any hint Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1j3t_3Y4iFjkXouNEHQLd1euJWlTzdWEoUG3WoZLDjonBHv…; http://secure-web.cisco.com/1uAkOO7CtOzygpinM5tt9ZZHkhl_HV3HHZnI2wodEWKz8oN… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] mri_glmfit DOSS
by Dr. Cornelius Kronlage 30 Jun '21

30 Jun '21

External Email - Use Caution Dear all, this error seems to be gdfCheckNPerClass in utils/fsgdf.cpp. Using "doss" or "DOSS" as a tag in the FSGD file doesn't help either, strangely. Could it be that it should be strcasecmp() instead of strcmp() in line 1046 of fsgdf.cpp? Cheers, Cornelius Date: Tue, 29 Jun 2021 15:19:20 +0000 From: "Dr. Cornelius Kronlage" <Cornelius.Kronlage(a)med.uni-tuebingen.de> Subject: [Freesurfer] mri_glmfit DOSS To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2a173629cd4540769ec6a07d892ca618(a)med.uni-tuebingen.de> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear freesurfers, for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD looks like this: GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ... When I try to run mri_glmfit I get the following error even though I specify DOSS: $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...] gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJk… INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case? Thank you! Best wishes Cornelius

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mri_seg_overlap error
by Javier Pozo 29 Jun '21

29 Jun '21

External Email - Use Caution Hello, I was trying to use mri_seg_overlap to find the DICE coefficient but, unless having FreeSurfer installed, I receive a "command not found" error when I try to run the tool. I hope you can help me. Regards, Javier.

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Re: [Freesurfer] Masking A Surface Overlay
by Jacoby, John 29 Jun '21

29 Jun '21

The "thresholding" options work well for thresholding a single overlay, but I would like to threshold one overlay using the values of a second overlay.

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