Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

mri_glmfit DOSS
by Dr. Cornelius Kronlage 09 Jul '21

09 Jul '21

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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recon-all soft errors
by Rosalia Dacosta Aguayo 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer team, I am inspecting the different participants I have run recon-all -all and I have found different errors I would like to discuss with you before proceeding as I am new with this software. 1. I have found dura at some regions of the brain. I should use gcut or delete voxels? 2. I have found discontinuity in GM and what I should do with this (attached photo 2) 3. In photo 1, not sure at some regions were to consider wm as it is not clear for me...any suggestion with this one? I think it should be done with cp, right? Kind regards, Rosie

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smoothing volume data extracted using aparcstats2table
by Ryan Bell, Ph.D. 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer Experts, I am wondering whether the extracted ROI volume data acquired when using the command aparcstats2table needs to be smoothed? I performed surface smoothing using surf2surf for cortical thickness data, but cannot find a way to smooth the volume data listed in aparcstats2table. Is it recommended that I do not perform smoothing? Thank You, Ryan ----------------------------------------------------------------------------------------------- Ryan Patrick Bell, Ph.D. Research Analyst, Department of Psychiatry & Behavioral Sciences 905 W. Main St., Suite 24-E Durham, NC 27701 Phone: (919) 681-3495 Email: ryan.bell(a)duke.edu<mailto:ryan.bell@duke.edu> Website: http://secure-web.cisco.com/1fzJIQLKPmbhrC2x32S5RRIKOnZE7eB318ehdee9qx2NWta… Twitter: twitter.com/HARPatDuke<https://secure-web.cisco.com/1K3qzDbdESi5BxKdIeeFsl0dti1McxRsbgZL6xE6fNf4Bc…>

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Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient and corresponding surface map
by Hye Min Shin 09 Jul '21

09 Jul '21

External Email - Use Caution Thank you for the response Bruce. I apologize for the confusion regarding surface map but what I was trying is that I wanted to create a surface file that contains dice coefficients for labels across the entire cortex. With your response, I think I can get the average dice coefficient for each label and hopefully create a surface map that visualizes dice coefficients on brain surface map. Would there be a way to create my own surface map with brain morphometry values that I created? Best, Julia Shin

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Cortical thicknees normalization values
by Gabbo Ramírez García 09 Jul '21

09 Jul '21

External Email - Use Caution Hi freesurfer user. I have been working with some cortical thickness values of a control group to test some changes related to cognitive training. However, I have been hesitating about whether I have to normalize the cortical thickness values (as happens with subcortical volumes and ICV) or not. I have read a little about it and I understood that I could use the ICV or/and mean cortical thickness, but I didn't find a specific criteria to do or not this normalization. Any clue, recommendation, explanation or paper about this will be very helpful. Thanks in advance. *or reposting discussion of this question. Gabriel R.

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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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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

1 0

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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Freesurfer June 2021