Re: [Freesurfer] Follow up question on group analysis (mri_glmfit)

External Email - Use Caution Yes, that is all correct. There is a tutorial on the wiki. You can use multiple covariates. See https://secure-web.cisco.com/1RwswV5KTgyno813OwbYPsChep2vyOd84uZhtCymnh_LaEd8jFvwUJVQOhDIhz80oOjWByV0_OhjirTD8kxhoc823Lx4-TGmNolu55PXDVE4KUKR50Zc2OldUaoPuSu

[Freesurfer] Follow up question on group analysis (mri_glmfit)

External Email - Use Caution Thanks for the quick response. So I followed the steps of the tutorial and performed group analysis by running mris_preproc, then mri_surf2surf and then mri_glmfit. Is that the correct way to do that? and in this case, can I include multiple continuous

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

External Email - Use Caution I can check to see if there is a license in the Freesurfer v5 Ubuntu VM I mentioned in the previous email and send it to you to try.   But per my last email, I don’t know a way to decode an old license on newer versions of the OS where glibc has been

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

External Email - Use Caution Hi! Would it be possible to obtain a license file for Freesurfer v5.3 that is compatible with the glibc versions on newer Linux systems? That would go a long way in resolving our issues. Thank you, Caspar __

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Thanks R, those are very good points. -Paul From: fsbuild Sent: Tuesday, September 13, 2022 2:21 PM To: freesurfer@nmr.mgh.harvard.edu Cc: r.lud...@eni-g.de ; Wighton, Paul ; fsbu...@contbay.com Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

vard.edu> on behalf of Ludwig, Rüdiger <r.lud...@eni-g.de>Sent: Tuesday, September 13, 2022 11:32 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu Hello again,I realized I might have missed som

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

ehalf of Ludwig, Rüdiger Sent: Tuesday, September 13, 2022 11:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu Hello again, I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago:

[Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again, I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago: We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/'' for freesurfer 5.3 When we try ''mri_convert sample-001.mgz sample-001.nii.gz

Re: [Freesurfer] follow-up on trac-all -prep -c error

d properly and if it needs to be updated. Hope this helps, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Friday, December 3, 2021 5:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] follow-up o

Re: [Freesurfer] follow-up on trac-all -prep -c error

External Email - Use Caution Sorry, I just realized that I sent a wrong trac-all.log and trac-all.error file. From: Salar Dini, Elaheh Sent: Friday, December 3, 2021 5:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: follow-up on trac-all -prep -

[Freesurfer] follow-up on trac-all -prep -c error

External Email - Use Caution Hello Anastasia, Thank you so much for your response. It was very useful. I have changed the config file to the one I'm attaching to this message, but I'm still getting the same error: ERROR: for B0 distortion correction with reverse-polarity DWIs ER

[Freesurfer] Follow-up: PVC to calculate myelin maps

External Email - Use Caution Dear FS-experts, I want to create myelin maps out of T1w/T2w contrasts and I have already read this e-mail conversation from the archive:

Re: [Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

Hi Kaley, the problem is,, when you re-run the base with different images, it will create the median image at a different location. That means that all your edits will be at the wrong location. I currently don’t see a way to fix this easily without a lot of tweaking of the recon-all script. On

[Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 ti

Re: [Freesurfer] (Follow-Up) Interaction Contrast

The two covariates (in theory) will account for some of the variance by themselves. You could get some bias if you don't includ ethem On 05/03/2018 03:33 PM, David S Lee wrote: > > > Dear Douglas, > Thank you for your guidance. > I am following-up on your response with regards to setting up DODS

[Freesurfer] (Follow-Up) Interaction Contrast

External Email - Use Caution Dear Douglas, Thank you for your guidance. I am following-up on your response with regards to setting up DODS matrix to test interaction between two continous covariates. If I understand your recommendation correctly (please correct me if I am wrong

Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg

On 10/25/15, 3:29 AM, "Jacobs H (NP)" wrote: >Hi. > >Just one another related question: now that I was able to combine left and >right hippocampal subfields with the aparc-aseg correctly, I noticed that >the left and right hippocampal subfields have the same color labels and >codes. What would

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve > Sent: Friday, March 13, 2015 11:01 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to > talaraich > > > > On 3/13/15 10:10 AM, Krieger, Donald N. wrote: &

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

.D. > Department of Neurological Surgery > University of Pittsburgh > >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- >> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve >> Sent: Thursday, March 12, 2015 4:25

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, March 12, 2015 4:25 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to > talaraich > > sorry, I don't know what you've done or what you

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[mailto:freesurfer- >> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve >> Sent: Thursday, March 12, 2015 3:44 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors >> to >> talaraich >&

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

r-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, March 12, 2015 3:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to > talaraich > > w

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

what do you want us to check? On 03/12/2015 03:27 PM, Krieger, Donald N. wrote: > > Dear List, > > I’ve done a couple of spot checks which appear to work but want to > double check with you. > > Attached are 5 axial cuts from fsaverage’s orig.mgz 5 mm apart. > > The “white” surface vectors are sh

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

] On Behalf Of Krieger, Donald N. Sent: Thursday, March 12, 2015 3:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] follow up and double check: transform RAS vectors to talaraich Dear List, I've done a couple of spot checks which appear to work but want to double check wit

[Freesurfer] follow up on question asked during freesurfer course

Hi To compare data different version of Freesurfer I was advised to bring it into the same version, and the subjects are the same. I used recon-all –make –all –s to convert from Freesurfer 4.30 to Freesurfer 5.1. The results are now more similar but there are some differences for weak corre

[Freesurfer] follow-up

...Also, I should mention that slice thickness in the MRI acquisition sequence was 1.3 mm so the native voxels are not 1x1x1. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] follow-up

not trivially, although it would be easy to do the replacement in matlab. It's because it binarizes the labels to 128 (which is Nerve in our LUT) On Mon, 16 Nov 2009, Jared Price wrote: > Thanks, I tried mri_extract_label and it works fine. However, it > extracts the structure and gives it the

Re: [Freesurfer] follow-up

I don't know about extract_label, but you can set the output value in mri_binarize Jared Price wrote: > Thanks, I tried mri_extract_label and it works fine. However, it > extracts the structure and gives it the label "nerve". Is there any way > within mri_extract_label to keep the original l

[Freesurfer] follow-up

Thanks, I tried mri_extract_label and it works fine. However, it extracts the structure and gives it the label "nerve". Is there any way within mri_extract_label to keep the original labels (i.e. left putamen, right putamen, or whatever)? Jared ___

Re: [Freesurfer] follow-up to Hausdorff distance question

it should be with the current version. If you tell us what hardware/software platform you are using we can send you a version Bruce On Thu, 16 Jul 2009, Jared Price wrote: Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that

[Freesurfer] follow-up to Hausdorff distance question

Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that could calculate it, but I don't see it in the /Applications/freesurfer/bin directory. Is it elsewhere? Is it included with 4.4.0? ___

[Freesurfer] Follow-up Question -- Multiple Comparison - Clusterwise Correction

Hi Doug, This is a follow up question regarding display issue from mri_glmfit-sim. The issue as you explained was that the original annotation was not being cleared. You suggested a short-term as well as a long-term fix. The temporary fix was deleting "-annot aparc" from mri_glmfit-sim. As a mor

Re: [Freesurfer] follow-up to automation of TkMedit

did you try calling RedrawAll? On Tue, 16 Sep 2008, Jared Price wrote: Hi everyone. This is Jared over at Brigham and Women's. I have a follow-up question on the question I asked earlier about automating TkMedit such that it will switch between the segmentation overlay view and the gray-scal

[Freesurfer] follow-up to automation of TkMedit

Hi everyone. This is Jared over at Brigham and Women's. I have a follow-up question on the question I asked earlier about automating TkMedit such that it will switch between the segmentation overlay view and the gray-scale MRI view automatically. I was able to find a scripting option that I