[Freesurfer] Along- tract multiple comparison result visualisation and summary interpretation

External Email - Use Caution Hello,I have questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2.1) I ran it and I found a significant result (see attached summary file) where I expected/found a negative association

[Freesurfer] Fwd: subcortical volume-based pet analysis

External Email - Use Caution Please, anyone able to answer these questions. Thanks a lot. Sent from my Samsung Galaxy smartphone. Original message From: miracle ozzoude Date: 2019-10-21 10:24 (GMT-05:00) To: Douglas N Greve Subject: subcortical volume-based

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. Original message From: "Greve, Douglas N.,Ph.D." Date:

Re: [Freesurfer] Fwd: remove skull from gtmseg.mgz

Thanks doug. Do I need to include a flag in gtmseg to change the colour? Best. Paul

Re: [Freesurfer] mri_glmfit error with aparc table flag

Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh "‎ and it worked. Best, Paul

Re: [Freesurfer] Fw: PETsurfer surface based analysis

Hello Doug, I was able to solve the problem. It had to do with the gtmseg part of the pipeline. I had to re-run gtmseg again and mri_gtmpvc exited without error and produced all output. Thank you Best, Paul

[Freesurfer] Fw: PETsurfer surface based analysis

Re: [Freesurfer] multiple expert options files/ wm and control points

Thanks doug. I know the -T flag in mri_fill means  min #of neighbors which must be on to retain a point/specify fill_holes threshold. What does it simply do if I use it in mri_fill‎?  Best, Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Wednesday,

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

Hello Antonin, Thank you very much for you help. I shall do it tomorrow and provide an update. Best, Paul.

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on

[Freesurfer] Fw: PETsurfer mri_coreg problem

[Freesurfer] PETsurfer mri_coreg problem

Hello Freesurfer, While checking the Coregistration step of PETsurfer using tkregisterfv, I encountered an issue (not sure if it was an error). The transform GUI simultaneously opened with freeview and I received this message in the terminal window  ( warning : transformation can only apply to

[Freesurfer] Control points and WM edits

Hello Freesurfer, I played around with mri_normalize for control point section by changing the parameters using -b 20 or 23 and writing it in an expert file. However, when I ran recon-all -autorecon2-cp -autorecon3 -expert expert.opts, the command showed "mri_normalize - mprage -noconform )

[Freesurfer] T2 and control points

Hello,  I ran the entire recon pipeline with T2 option and then added control points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the pial surface or not? Thanks.  Paul Sent from my BlackBerry 10 smartphone. ___ Freesurfer mailing

[Freesurfer] Fw: White matter probability map. ( REPOST)

Re: [Freesurfer] White matter probability map.

Hello Douglas,  Thank you. When I looked up the command with --help, it said " computes partial volume fractions for cortex, subcortical GM, WM and CSf". What volume do I give the command as an input? T1, orig.mgz ‎.  Best,  Miracle Sent from my BlackBerry 10 smartphone.   Original Message  

[Freesurfer] White matter probability map.

Hello Freesurfer, Is there a way to extract tissue probability map for  white matter   in FS. Thank you Best, Miracle Sent from my BlackBerry 10 smartphone. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Stable version of freesurfer 6.0

Hello. I noticed that the stable version of FS 6.0 was released today however, the release was dated  January 23th, 2016. Shouldn't it be January 23th, 2017? Best,Paul Sent from my BlackBerry 10 smartphone. ___ Freesurfer mailing list

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

another question. How do I incoporate -cover_seg into it? do i need  surfaceRAS coordinates? On Mon, Jan 9, 2017 at 5:04 PM, miracle ozzoude wrote:Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value? Best, 

[Freesurfer] Edit to wm.seg.mgz.

Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon-all -autorecon2-wm -autorecon3 -s fsdir ( I know -autorecon2 -wm is used when you make edits to wm.mgz) or should I just run recon-all

Re: [Freesurfer] recon-all -autorecon2 error.

Awesome. Thank you very much Bruce. Sent from my BlackBerry 10 smartphone.   Original Message   From: Bruce Fischl Sent: Monday, November 28, 2016 5:14 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] recon-all -autorecon2 error. -rl is for "reslice

Re: [Freesurfer] recon-all -autorecon2 error.

Thanks a lot Bruce. What do you mean by -rl and how do I incorporate it to mri_convert?   Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Bruce Fischl Sent: Monday, November 28, 2016 4:57 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re:

Re: [Freesurfer] Fw: recon-all steps question

Thank you very much Bruce. Last questions. When I replace FS generated brainmask.mgz with mine, does the original also remain in the mri folder( that's having 2 brainmask.mgz)  or  is the original permanently replaced with my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)?

Re: [Freesurfer] Fw: recon-all steps question

Thank you very much Bruce. Last questions. When I replace FS generated brainmask.mgz with mine, does the original also remain in the mri folder( that's having 2 brainmask.mgz)  or  is the original permanently replaced with my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)?

Re: [Freesurfer] Fw: recon-all steps question

Thank you very much Bruce. Last questions. Any reasons why you suggested I avoid " - no" flags? This is because I searched through the forum and it seem the " -no flag" was  encouraged whenever someone wanted to replace FS generated volume with their own, especially in the case of skull

Re: [Freesurfer] Fw: recon-all steps question

Hence, you are saying I should run recon-all -autorecon1 -i -s subjid then replace the FS generated  brainmask.mgz with my own stripped volume. Also, should I run recon-all -autorecon2 with wm segmentation ( after replacing the stripped volume ) and replace FS generated wm.seg.mgz with my wm

Re: [Freesurfer] Fw: recon-all steps question

Thank‎ very much Bruce. Does it mean I have to run recon-all -autorecon1   -noskullstrip, then recon-all -autorecon2 -nosegmentation ( with the skull stripped volume) . Finally, recon-all -autorecon2-wm -autorecon3 -s subjid( with the wm and lesion stuff)? Thanks ‎ Sent from my BlackBerry 10 

Re: [Freesurfer] Fw: recon-all steps question

We have already skull stripped and white matter segmented volume ( used lesion explorer) . Hence, I want to replace freesurfer 's generated outputs for this steps ( brainmask.mgz for skull strip and wm.seg.mgz (not wm.mgz ) for white matter)  ‎with ours. I know recon-all -all performs all 31

Re: [Freesurfer] Fw: recon-all steps question

Thanks Bruce. Another question, since " -no segmentation " flag skips the white matter segmentation step of recon-all. Can I also use the same logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's, run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then

[Freesurfer] Fw: recon-all steps question

Please can someone answer this. Thanks " Hello Freesurfer, I have couple of

[Freesurfer] Fw: recon-all steps question

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Thanks doug. Also, let's say I extract the aparcstat table and perform t -test using spss and a ROI become significant, is it possible the significant effect will be lost using GLM surface based?  Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve

[Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Hello freesurfer experts,  What's the difference between GLM surface based cortical thickness analysis and the cortical thickness analysis performed when using regions extracted from aparcstat table? Best, Paul Sent from my BlackBerry 10 smartphone. ___

Re: [Freesurfer] malloc_error_break/ can't allocate region

Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1? Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Tuesday, August 16, 2016 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

Hello doug, Should I add --label-src in addition to --label-trg or should I replace the latter with the former? Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim.   Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent:

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

Thank you doug. Is there a command for normalising in fsgd file. I know DeMeaning is DeMeanFlag 1.  Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Friday, July 22, 2016 6:45 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support