Re: [Freesurfer] Using the Desterieux Cortical Atlas to Extract PET SUVs

/cvs_avg35_inMNI152/mri/aparc.a2009s+aseg.mgz be what I’m looking for then? Best, Hannah From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Date: Monday, March 27, 2023 at 10:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using the Desterieux Cortical Atlas

[Freesurfer] Using the Desterieux Cortical Atlas to Extract PET SUVs

of the cingulate cortex then we would like to use (just anterior/posterior). Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer? I would really appreciate the help. Best, Hannah -- Hannah Bues (she/her) Clinical Research Coordinator

Re: [Freesurfer] Freesurfer Website Ports

ite? that is not needed to run FS > > On 4/5/2021 3:20 PM, Swearingen, Hannah wrote: > > External Email - Use Caution > Hi, > > I am setting up an Access Control List for an isolated VLAN in which my > center's neuroimaging computing workstations will be connected

[Freesurfer] Freesurfer Website Ports

a security breach, and they are wondering if we will still be able to access the website without the 21/FTP port opened? Can anyone provide me with that information? Thanks, Hannah -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] FDR correction for statistical maps in Freeview?

External Email - Use Caution Dear all, I am using glmfit to analyse changes in cortical thickness, but I couldn't find a description on how to perform FDR correction with FreeSurfer. Is there a way to perform FDR correction of the statistical maps in Freeview, analogous to how

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

try it > with --no-dwi and see if it runs to completion? If it does, do you have > another way to get the bvals and bvects? > > On 1/26/2021 3:33 AM, Hannah Eichhorn wrote: > > External Email - Use Caution > > Thanks for your answer! > > The full c

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution Thanks for your answer! The full command line is: mri_convert /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA /indirect/data1/hannah/Test

[Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

have any thoughts on how to solve this error? I am using FreeSurfer version:  freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you, Hannah Eichhorn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] Welch's t-test for HOV violation

ght that you want to do this on a voxel-wise basis. doug On Thu, Mar 14, 2019 at 10:10 AM Hannah CK wrote: > Hi Dr. Greve, > > Sorry about that - I had followed the "Reply via email" link on the archive > page instead of posting to the forum directly. > > Tha

Re: [Freesurfer] Welch's t-test for HOV violation

the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-13 Thread Greve, Douglas N.,Ph.D. Hi Hannah, plea

[Freesurfer] Welch's t-test for HOV violation

External Email - Use Caution We are conducting t-test comparisons across groups in which there is a large discrepancy in group sizes. HOV is violated. I've searched for ways to run Welch's t-test in FreeSurfer (or a similar analysis that does not assume homogeneity of variance)

[Freesurfer] Report Effect Sizes of Significant Clusters - using .mgh files

We used the gamma.mgh and rstd.mgh files to derive an effect size file that we called cohensd.mgh. How can I access these files to report effect size (Cohen's *d*) for significant clusters? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Andrew, thanks for your reply. Yes, I am using bash and my operating system is Mac OS X 10.9.5. Could you direct me how to set a path correctly? I ran recon_all fine. On Wed, Jan 24, 2018 at 1:14 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Hannah, > > > > Wha

[Freesurfer] Acquiring Exact p Values

Hello, I am conducting surface group analyses and would like to acquire exact p values. The FreeSurfer manual notes that the number listed after the peak coordinates and the vertex # is a "significance value," and that the "significance in this display is a -log(10)p value, and not a straight p

[Freesurfer] Trac-all Image Correction error

Hello, I keep receiving an error when I try to run 'trac-all -prep -c dmric.trac' The error I receive says that dwi_orig_flip.mghdti.bvecs can not be moved but in the code it is never created. Is there a way to manually create this file? I have tried to manually run the code and edit the dmric

[Freesurfer] SAG FSPGR BRAVO Sequence

Hello, Has anyone processed a SAG FSPGR BRAVO sequence successfully through FreeSurfer? When I run these images the program finishes without error however the output in tksurfer is grossly incorrect. Is there a way to adjust the parameters for reading white and gray matter by freesurfer

Re: [Freesurfer] SAG FSPGR BRAVO Sequence

On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ashley if you upload a dataset we'll take a look. I am surprised to hear that you are having problems. Can you post an example image? Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote: Hello, Has anyone

Re: [Freesurfer] SAG FSPGR BRAVO Sequence

These are in norm.mgz format On Wed, Oct 30, 2013 at 2:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ashley what format are these in? They don't have an extension thanks Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote: Here are the tkmedit with overlay images. Thank you

[Freesurfer] bug reporting

with ERRORS at Thu Jul 25 11:15:50 CDT 2013 thanks in advance for your input, - Hannah Kyllo The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have

[Freesurfer] (no subject)

Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- * * ___ 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

[Freesurfer] Help -- asegstats2table error, Please Help

do not understand this error message. Does anyone know a way around this? Ashley Hannah * * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

[Freesurfer] qdec GLMDesign Problem

/bruehh01/Borderline_2/qdec/Untitled Since I haven't changed anything since I last ran analyses, I don't understand what the problem is. Any suggestions? Thanks and regards, Hannah

[Freesurfer] Skullstrip Delay

translation: (-1.1, -8.0, -23.9): log p = -22300.7 Nine Parameter search. iteration 0 nscales = 0 ... without an error message, I have no clues as to how to fix this problem. Any suggestions would be much appreciated! Thank you so much, Hannah

[Freesurfer] mris_anatomical_stats question

Hi there, I have got 2 questions: 1) is there way to use mris_anatomical_stats to map back the label I have created onto all the subjects in my directory simultaneously? I know there is the --subject option but how do I then specify the directory for each individual subject? 2) I tried to

[Freesurfer] qdec problem

Hi, I have a problem using qdec, which I don't know how to solve- I get the following error message: Error in Analyze: command failed: mri_glmfit --y /Users/Hannah/ Borderline/subjects/qdec/Untitled/y.mgh --fsgd /Users/Hannah/ Borderline/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Users