Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?

ainers for this client From: fsbuild Sent: Tuesday, July 25, 2023 5:18 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Salomon, Ryan Subject: Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS? My understanding is no environment variab

Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?

From: fsbuild Sent: Tuesday, July 25, 2023 5:18 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Salomon, Ryan Subject: Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS? My understanding is no environment variable setting like

[Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?

External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter t

[Freesurfer] Passcode Request

External Email - Use Caution Hello, I am trying to extract files in the 7zip download for the VurtualBox VM and it requires a passcode. Could you please send me the passcode required for this step. Thanks, Ryan ___ Freesurfer mailing

Re: [Freesurfer] VirtualBox appliance 7z pass code

External Email - Use Caution Hello, any chance I could get the pass code? I'm really hoping to start my project soon, and I haven't been able to get Freesurfer running from scratch. On Fri, Jun 17, 2022 at 2:05 PM Ryan Johnson wrote: > Good afternoon! > > I

[Freesurfer] VirtualBox appliance 7z pass code

External Email - Use Caution Good afternoon! I would like the pass code to unzip the FreeSurfer 7 VirtualBox VM. Thank you, Ryan Johnson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Color LUT after coregister and reslice aparc/aseg.nii

r each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Ne

[Freesurfer] smoothing volume data extracted using aparcstats2table

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

Re: [Freesurfer] Freesurfer on new Mac (apple silicon-chip)

Hi Vânia, Currently, I am running 7.1.1 (the most recent release) on Big Sur without issue. I’m not sure we can speak to the stability when running it on the new Arm chips given they were just released though if you had issues a virtual machine can serve as an alternative. Cheers, Ryan

[Freesurfer] Extracting PET Binding Values from Inflated Surface

extract average values from surface ROIs as defined by the ?h.aparc.annot file? Thanks! Ryan O'Dell MD/PhD PGY4 Psychiatry Resident, Yale University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

Thanks Doug! When you say sample onto the mni152 surface, you mean to use mri_vol2surf, correct? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On May 27, 2020, at 11:10 AM, Douglas N. Greve wrote: >

[Freesurfer] Registering Mean Diffusivity to Anatomical Space

map to subject space Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

ree scenarious (gtm, no pvc, and mgx)?" So I added the uptake values for the cerebellum to the original table, which I've pasted below. Let me know if there's anything else you need. Thanks! Ryan vol | psf | roi |

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

ortex | 1.016 | 1.01104 mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 0.915328 mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 0.809017 Thanks! Ryan From: freesurfer

[Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

s is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan vol,psf,roi,gtmstats_uptake,mean_uptake input.rescaled.nii.gz,0,ctx-rh-pericalcarine,0.807,1.2259972095489502 input.rescaled.nii.g

[Freesurfer] LGI help

RORS at Tue Mar 3 11:09:41 PST 2020 For more details, see the log file /working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your time, Ryan Michael Nillo Staff Research Associate I University of Cali

[Freesurfer] freesurfer linux-ppc build

External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

matrix with only one of the two groups and have a pcc.mgh for that analysis. When I compare that to the pcc.mgh I get from my original analysis for that same group, the value at each vertex is slightly different. Ryan Michael Nillo UCSF Department is Radiology and Biomedical Imaging Lab for

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

Am I correct in assuming this results in z-scoring/normalizing the covariates? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. > wrote: > >

[Freesurfer] mri_glmfit ill-conditioned matrix question

above Attempting to diagnose further SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4) ... could not determine the cause of the problem Can anyone give me some insight into what might be going wrong? Thanks so much, Ryan Michael Nillo Staff Research Associate I University of California San Fran

[Freesurfer] Question on Z-scoring

, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer

[Freesurfer] Converting a binary overlay file to label

External Email - Use Caution Hello FreeSurfer users/developers. I manually created a binary overlay file on the pial surface. I am interested in looking at regions outside of this overlay file, so I converted lh.cortex.label to a binary overlay file and took the difference betwe

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

Pial-outer-smoothed was a surface created from recon-all -localGI. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. > wrote: > > how wa

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

advance for the help, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D. > wrote: > > Who did you create lh.test.nii? > > On 7/1/2019 1:47 PM, N

Re: [Freesurfer] Surfaces with different numbers of vertices.

-localGI on to get the pial-outer-smoothed surface. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 10:27 AM, Bruce Fischl wrote: > > Hi Ryan > > I'm not sure why you would

[Freesurfer] Surfaces with different numbers of vertices.

with less vertices? Is there a way to map values from the 73,000 vertices-map to the standard fsaverage pal surface? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S

[Freesurfer] Help for smoothing the pial surface

ant to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature Ex

[Freesurfer] Smoothing the pill surface

an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution

Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller compared to those without the heterotopia. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On May 15, 2019, at 3:10 PM, Bruce Fischl

Re: [Freesurfer] Color scale error

External Email - Use Caution Toggling the colorbar on and off in the GUI updates the values and appearance. Changing the threshold also seems to work once I press the “apply” button on the configuration window. Ryan Michael Nillo Staff Research Associate I University of

Re: [Freesurfer] Obtaining stats for a custom label

External Email - Use Caution Correction to the previous email: I can view the label in the rh.white, not lh.white.  Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Apr 24, 2019, at 10:50

Re: [Freesurfer] Obtaining stats for a custom label

--i /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii --id 1 --l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and

[Freesurfer] Obtaining stats for a custom label

values for any of the metrics listed above. Is this a bug? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer

[Freesurfer] Projecting a subcortical label to the surface

to the fsaverage cortical surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] mri_vol2surf error

getting this error: mri_vol2surf: could not read surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am trying to project to the surface of the fsaverage. Does this error mean that FS is unable to find the fsaverage surface? Ryan Michael Nillo Staff Research Associate

[Freesurfer] pial surface and eTIV

surfaces or if that does not matter. Important to note, at the moment, I'm only interested in pulling hippocampal volumes and eTIV (to get relative hippocampal volumes). Similarly, would poor pial segmentation affect the reported hippocampal volumes at all? What do you recommend? Thanks, Ryan

[Freesurfer] Color scale is off

configure step. Example command line: freeview -f fsaverage/surf/ph.pial:overlay=lh.thickness.betas:overlay_threshold=0,0.05:overlay_method=linear -colorscale -ss lh.lateral.thickness.beta.tiff Thanks in advance, Ryan Nillo ___ Freesurfer mailing list

[Freesurfer] Should I edit or reject?

with this logic? Thanks for your advice, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing

Re: [Freesurfer] Setting the origin in native space

External Email - Use Caution Thanks for your help, Bruce. This worked like a charm! How would I register the output segmentation back to the subject's T1.mgz? When I use mri_convert, the ROIs have a weird border around them. thanks again,

[Freesurfer] Setting the origin in native space

Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image? Thanks in advance, Ryan Nillo Staff Research Associate UCSF Department of Radiology and Biomedical Imaging

[Freesurfer] Using the SUIT atlas

centered at the anterior commissure. Does FreeSurfer have any tools to set this origin from the command line? Thank you for your help, Ryan Nillo Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer

[Freesurfer] re-run fsaverage only

that each have a different subset of my participants, but I'd like there to be one directory that has all my participants. Is there any command that I could run that would generate a new fsaverage from subjects in the same output directory? Thanks, Ryan Wales -- Ryan Wales Graduate Student Cog

[Freesurfer] Extracting values from a single vertex

mris_convert on it, I only got the value at a vertex on the first frame. The goal is to set that vertex as a seed point and use the values as a regressor for glm. Is there a way to do this with FreeSurfer's commandline tools, or should I do this in Matlab? Mahalo, Ryan M Nillo

Re: [Freesurfer] automating custom color map

External Email - Use Caution Thank you so much, Ruopeng. Do you have an estimated timeline for when this option might be done? Ryan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang Sent: Thursday, November 1, 2018 7:18

[Freesurfer] Research Opportunity

e at leo.sug...@ucsf.edu<mailto:leo.sug...@ucsf.edu> Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] Designing Constrats for 3 Group 1 Covariate Analysis

of analysis is also likely QDEC-able, but I think the FSGD approach would be more beneficial for my understanding of contrast matrix design. Please let me know if I've left out any information that could potentially help clarify my question/request. Best, Ryan O'Dell MD/PhD PGY2

Re: [Freesurfer] hippocampal subfield segmentation

freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Tuesday, August 21, 2018 3:17:15 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation External Email - Use Caution Hi Ryan, Is it possible that you'r

[Freesurfer] hippocampal subfield segmentation

ror in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar

[Freesurfer] Thickness measurements.

External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a way to use white and pial surfaces not generated from the mris_make_surfaces to create thickness files? Mahalo, Ryan M Nillo Staff

[Freesurfer] Longitudinal Processing question

nal directories? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] mri_glmfit question

the ROIs and output tables showing significance. In each contrast directory that was created from mri_glmfit, I see there is a pcc.mgh. Is there any way to display this on the surface or put it into a table format? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

ROI? Is there a way to also obtain non-segmented stats? Also, the reason I didn't map the ROI to fsaverage was because I didn’t have access...is there a way to change that? Thank you for your time. Best, Ryan -- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:32

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

External Email - Use Caution Great. That seemed to have worked. Is there a way to inspect that the ROIs have been correctly placed? Perhaps by using freeview? Best, Ryan -- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM, "freesurfer

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

las.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help. Best, Ryan -- Ryan Flore

[Freesurfer] Cortical Thickness Using N30R83 Atlas

vant. Any advice would be greatly appreciated. Thank you for your time. I look forward to hearing from you. Best, Ryan -- Ryan Flores Clinical Research Coordinator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is greatly appreciated. Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

help is greatly appreciated. Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

External Email - Use Caution Hi Doug, I just wanted to follow up on this. Were you able to download the zip file ok? Best, Ryan On 4/18/18, 10:46 AM, "Ryan Flores" wrote: Yes, of course. Please see attached. Best, Ryan -- R

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

Hi Doug, Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference. Best, Ryan -- Ryan Flores Clinical Research Coordinator From: on behalf of

[Freesurfer] localGI issues

ata/sugrue2/NF1_qdec/sub_0015/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your time, Ryan Nillo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

[Freesurfer] LGI error

st= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); Sincerely, Ryan Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.ha

Re: [Freesurfer] mri_glmfit mask.mgh for mri_surfcluster

Perfect --- Thank you! Ryan > On May 15, 2017, at 6:09 PM, Douglas N Greve > wrote: > > usually the fsaverage mask is fine. You can use mri_label2label with the > --outmask option to convert the ?h.cortex.label to a binary mask. You > can also pass surfcluster a label

[Freesurfer] mri_glmfit mask.mgh for mri_surfcluster

should we be creating a mask that is specific to a given analysis/dataset, as is done with mri_glmfit? If the latter, is there a way to create this mask outside of mri_glmfit? Thank you in advance for your time and help! Best, Ryan ___ Freesurfer m

[Freesurfer] -hemi flag

, white matter is missing in the half of wm.mgz not specified under the -hemi flag, but the surfaces and segmentation in aparc+aseg are unaffected. Is this a bug? Ryan Michael Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate

[Freesurfer] v6 Hippocampal subfields on a cluster

the 2-3GB range, do you happen to know of any flags I can/should pass to java/MCR to limit the parallel/memory expectations? For example, I’ve tried: export _JAVA_OPTIONS="-XX:ParallelGCThreads=1”, but without any luck. Let me know if you have any suggestions! Al the best,

Re: [Freesurfer] error loading surface on one machine, but not another

Yes, and they indeed do not match up on the two machines. I transferred twice, not sure why there would be this issue with just the lh files. I changed ftp programs and that seems to work. Thanks for pointing me toward in the (now) obvious route of doing the checksums. Cheers, Ryan On Dec

[Freesurfer] error loading surface on one machine, but not another

rfaces load fine on the second machine. I've double checked that the files were copied completely and were not truncated. Has anyone experienced something similar or have an idea of what is going on? Thanks! Cheers, Ryan ___ Freesu

[Freesurfer] localGI & Matlab runtime?

allelize" this (i.e., run different subjects on different cores) without using up many matlab licenses? Thank you! All the best, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] Optseq2 design question - series of events

Hi all - I'm trying to design my first event related experiment, and I'm having trouble figuring out how to best optimize the design...wondering if you have any insights: I have two conditions (milkshake and water). Each condition has several events in order: Participants get a squirt of milksha

[Freesurfer] Training Comparison

f the lh.thickness and rh.thickness files with the lh.long.thickness-rate files, but it gives me the following error: MRISreadBinaryCurvature: incompatible vertex number in file /Applications/freesurfer/subjects/7107-60_base/surf/lh.thickness ERROR: reading curvature file --

Re: [Freesurfer] (no subject)

; > > On 11/02/2012 11:34 AM, Ryan wrote: > >> Doug, >>I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd >> fsgd doss --C training-effect.mtx >> >> >> On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve < >>

Re: [Freesurfer] (no subject)

Doug, I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve wrote: > > > On 11/01/2012 06:35 PM, Ryan wrote: > >> Doug, >>Picture 4 shows the difference between the

Re: [Freesurfer] (no subject)

Doug, Here are the files. On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve wrote: > Can you send the command line and attach the files? > thanks > doug > > > On 11/01/2012 01:11 PM, Ryan wrote: > >> Doug, >>I tried running mri_glmfit-sim without the -

Re: [Freesurfer] (no subject)

. -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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

Re: [Freesurfer] Files

? >> Maren >> >> On Oct 30, 2012, at 4:22 PM, Douglas N >> Greve> >> wrote: >> >> Hi Ryan, I don't understand your model. This does not look like a >>> standard repeated measures ANOVA. Is it supposed to be equivalent? >>> dou

Re: [Freesurfer] Files

ysis with the contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Tue, Oct 30, 2012 at 11:28 AM, Douglas N Greve wrote: > Hi Ryan, I'm a little lost here. Can you resend your X and contrast > matrices and explain what each column is? > doug > > > On 10/26/2012 03:4

Re: [Freesurfer] Files

rst tells you if > controls are thinning (blue) or thickening (red), the 2nd tells you if the > training is doing the same. > doug > > > On 10/25/2012 03:34 PM, Ryan wrote: > >> Doug, >>Yes, it's a longitudinal study since we MRI participants pre-training &g

[Freesurfer] Training-Control Group Comparison Analysis

variables. Thanks for the help. -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it

[Freesurfer] Comparing cortical thickness for 2 groups

n run mri_glmfit? Thank you. Best, -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addresse

[Freesurfer] (no subject)

ds such as cluster corrections? Best, -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is add

[Freesurfer] (no subject)

RROR -10 : mris_calc compute sym. pct. change (spc) problem?", any thoughts? Thanks all. -- -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-

[Freesurfer] (no subject)

with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] repost: error using recon-all function

Freesurfer Experts, I am reposting an error message that I receive when using the recon-all function to analyze my own data. The command which I am trying to execute is: recon-all -s 2645166 -all 2645166 is the patient ID. Running this gives an error: ERROR: avi2talxfm failed, see transforms/ta

Re: [Freesurfer] error using recon-all function

Freesurfer experts, I emailed last week with an error using recon-all. This problem has still not been resolved. The summary of the problem should be shown below: Thanks, Ryan On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten < ryanhutten2...@u.northwestern.edu> wrote: > > > -

[Freesurfer] error using recon-all function

Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-al

[Freesurfer] uniform sampling of the sphere

Thanks in advance! Ryan Muetzel University of Minnesota ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is add

[Freesurfer] DTI group analysis

greve Exp $ cwd /Applications/freesurfer2/subjects/4964-59 cmdline mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir sysname Darwin hostname ryan-mcgarry

[Freesurfer] DTI group analysis

greve Exp $ cwd /Applications/freesurfer2/subjects/4964-59 cmdline mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir sysname Darwin hostname ryan-mcg

[Freesurfer] DTI Analysis

ndering if this is the correct usage for the sig.mgh file, and if someone could point me in the right direction for what steps are next? Thank you. -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?

ny idea of what's going on here? I find it perplexing that it's searching for a ribbon.mgz rather than an ?h.ribbon.mgz, since I found no evidence on the wiki of a file just called ribbon.mgz Ryan On Fri, Mar 27, 2009 at 4:49 PM, Bruce Fischl wrote: > yes, the thickness is ind

Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?

t way, since the thickness files are generated earlier in the recon stream. I ask this because we are trying to get the stats as fast as possible without having to rerun all of our cases (200+) over again. Ryan -- Forwarded message -- From: Bruce Fischl Date: Fri, Mar 27, 2009 at 2:

Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?

my FS version (3.0.4). You may have already read it, I'm not sure, but just in case, it's inline with this email. The file I uploaded is named 5008-003-02_scotton.tar.gz Thanks so much for your help, Ryan On Thu, Mar 26, 2009 at 5:36 PM, Bruce Fischl wrote: > Hi Ryan, > >

[Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?

pancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Version Discrepancies in Cortical Thickness Analysis?

/grey matter surfaces and cortical thickness measurements? If not, spectacular. If so, is there only a small portion of the recon-all stream that we could run so that we could take care of this problem as fast as possible? Thanks! Ryan ___ Freesurfer

Re: [Freesurfer] Viewing atlas?

late image that has already been parcellated appropriately in order to get the best idea of where each label lies. Is this an option? Ryan On Fri, Oct 24, 2008 at 12:26 PM, Doug Greve <[EMAIL PROTECTED]>wrote: > If you've reconned a subject, you can use the aparc+aseg.mgz volume. &g

[Freesurfer] Viewing atlas?

the FS parcellation/labeling scheme applied to it in order to get a general idea of how the separate labeling schemes match up? Thanks! Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Cortical thickness issues

ssing something on the best way to fix white and pial surfaces when they're not accurate enough. Could anyone offer me some advice/a link to a site which explains the best way to handle such problems? Thanks, and sorry for the long post. Ryan __

[Freesurfer] total brain volume correction

models. Both methods seem reasonable, but it seems entering total brain size as a covariate may be more robust, controlling for potential interactions with other IVs (e.g. age, gender). Are there other strategies I am missing? Any advice is much appreciated! Thanks! -Ryan

Re: [Freesurfer] wmparc/white matter problems?

Hi Doug, The white matter in aseg seems to follow the same pattern as the white matter in wmparc...it goes into the ribbon (through the white matter surface into gray matter). -Ryan On Dec 7 2007, Doug Greve wrote: Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they

[Freesurfer] wmparc/white matter problems?

the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)? Any help is much appreciated! -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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