[Freesurfer] the result of '1 -1' and '1 -1 0 0 0 0' are different

External Email - Use Caution Hi friends, (1) I have two groups, I set '1 -1' in .mtx file. (2) I add two variables in the .fsgd file, and set '1 -1 0 0 0 0' in the corresponding .mtx file. While, after run mris_preproc, mri_glmfit, I found the result of (1) and (2) are different

[Freesurfer] Does freesurfer must use 3-D T1

External Email - Use Caution Hi teams, Does freesurfer must use 3-D T1 to calculate cortical thickness? Thanks___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while control group from another acanner

External Email - Use Caution Hi friends, Using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while control group from another acanner? Thanks.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar

[Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

dvice! best regards, John ______ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552

Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John > On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl > wrote: > > Hi John > > the MEFLASH neve

[Freesurfer] mri_volsynth

res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ? 3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?     Thanks in advance , John ___ Freesurfer mailing list

Re: [Freesurfer] mri_volsynth

, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, August 31, 2015 at 11:30 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.h

Re: [Freesurfer] mri_volsynth

Thank you! Actually when I run mri_volsynth --help I can't find --revol. is it the same flag --res? also what is the relationship between --dim and --volres?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinma

Re: [Freesurfer] mri_volsynth

Perfect! Thank you very much for your help. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, August 31, 2015 at 4:30 PM

[Freesurfer] recon-all

?) 3. If there is any atlas that can separate the outer and deep white matter then do the segmentation depending on this new atlas.     Thanks in advance for any suggestion, John    Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419

[Freesurfer] Segmenting deep and outer white matter

s and the outer white matter labels ?) 3. If there is any atlas that can separate the outer and deep white matter then running recon-all depending on this new atlas.   Thanks in advance for any suggestion. John    Bests, John Anderson Senior Research Associate Psychological and Brain Sciences

Re: [Freesurfer] Segmenting deep and outer white matter

ce that can help. The number of the parcellate is very big and for the purposes of publication I need a reference to divide them.     Any help is highly appreciated.   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Bo

Re: [Freesurfer] Segmenting deep and outer white matter

labels for one of my subjects.     Bests, John Anderson Senior Research Associate  Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, September 07, 2015 at 1:02 PM From: &

[Freesurfer] White matter volume

  Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 4and the white matter volume generated by other methods like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603

[Freesurfer] Tracula_weighted dti metrics values

nii.gz -m >This command will output the mean FA for the probabilistic distribution map. How can I weight this FA value using the previous command line?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Ha

[Freesurfer] Basal ganglia

separatly? Is there any tool in Freesurfer that can help? Thanks for any suggestion.   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419

Re: [Freesurfer] correct thinking?

Hello, What is ICT ? Thanx On Jun 1, 2016 4:21 PM, "Marja Caverlé" wrote: > Hi Bruce, > > Thanks for your answer and all your help, I only want to look at cortical > thickness for now. > > Best, > > Marja > > On Wed, Jun 1, 2016 at 11:11 PM, Bruce Fischl > wrote: > >> Hi Marja >> >> yes, if you

[Freesurfer] Break 3D volume

Dear FS Experts, Are there any tools in Freesurfer or Matlab scripts that can help to break down a 3D volume ( created using mri_volsynth) to a multiple equal sub volumes ( like the attached figure ) Thanks in a dvance for any suggestion! John Anderson Senior Research Associate Psychological

Re: [Freesurfer] Break 3D volume

very much for your help     John    Sent: Wednesday, June 08, 2016 at 9:13 AM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Break 3D volume Hi John I'm not exactly sure what you mean, but you can use mri_extract to pull out rectangul

Re: [Freesurfer] Break 3D volume

Thank you Bruce... This is very helpful!   Bests, John Sent: Wednesday, June 08, 2016 at 9:32 AM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Break 3D volume the help is old! should be . (x0,y0,z0) is the starting point of your boundin

[Freesurfer] Freesurfer Help

it shows that I've selected a different color) it still draws/paints black on my image? Thank you for time and help!-John M.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inf

[Freesurfer] BERT is not working correctly with the toolbox list below the brain

  When I open freesurfer and type the command to pull up bert the brain pops up but the toolbox (icons) below it that are supposed to come up as well do not? Help is appreciated! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] smoothing T1 images

Hi FS experts, I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images. Thanks for any advice! B

[Freesurfer] X11 / mesa update broke tkmedit snapshots

27;re working now on figuring out a strategy to downgrade these, and some others. It's a little hairy because there are a lot of dependent packages and a lot of affected machines. If anyone else has seen this, or knows how to fix it, I'd love to hear from you. John Flavin __

Re: [Freesurfer] X11 / mesa update broke tkmedit snapshots

I should add that we're running tkmedit using xvfb since the process is automated and runs without a physical screen. Flavin > On Jun 22, 2016, at 4:15 PM, Flavin, John wrote: > > Hi all, > > I run the pipelines for the CNDA and various other XNAT installations. We > r

[Freesurfer] Qdec-correction for multiple comparison

any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)   Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207

[Freesurfer] Qdec-correction for multiple comparison

montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)   Thank you very much for any comment! John Anderson Senior

[Freesurfer] Qdec-correction for multiple comparison

montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)   Thank you very much for any comment! John Anderson Senior

[Freesurfer] Qdec-correction for multiple comparison

thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)   Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College

Re: [Freesurfer] Qdec-correction for multiple comparison

R and mote carlo simulation? Does "empirical " means to follow the results that support the hypothesis?       John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9

[Freesurfer] white and gray matter masks

and the file ribbon.mgz the output of recon-all to create a a mask for global gray matter   Thank you for any advice!   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603

[Freesurfer] QA tools

wrong authentication. GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0     At the end it said that he process finshed. I checked the AQ folder and the snaps where not there    Any suggestions!   Bests, John  ___ Freesurfer

[Freesurfer] Volume or surface?

lp     Bests, John  ___ 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-m

[Freesurfer] surface based analysis for subcortical structures

. How can I resume tha analysis for subcortical structures? Thank you for any help! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] de-identify DICOM

Hi FS experts, I wanted to inquire if there are any tools in FS that can help to de-identify DICOMs?     Thank you for any comment John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] FS download for Windows

version of VB with these files? If not, what should I do when I download the package this time? Thanks, Jack Hettema John M. (Jack) Hettema, M.D., Ph.D. Associate Professor Virginia Institute for Psychiatric and Behavioral Genetics Department of Psychiatry, Virginia Commonwealth

Re: [Freesurfer] surface based analysis for subcortical structures

DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 10.682767 ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd   I smoothed just fwhm = 1   Kindly how can I troubleshoo? thank you for any advice   Bests, John 

[Freesurfer] Fw: Re: surface based analysis for subcortical structures

--cwpvalthresh .0166 All the bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Thursday, October 20, 2016 at 9:20 PM From: "

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

why I want to use "mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166"   Bests, John  Sent: Friday, October 28, 2016 at 11:53 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcort

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

than never:). But in the end, you probably want to use permutation if your group analysis allows it.     On 10/23/16 10:25 AM, John Anderson wrote: Thank you very much Doug, The codes worked very well. I was using the wrong command to correct the data. My command was  mri_glmfit-sim --glmdir s

[Freesurfer] recon all

=0.0344, pval=0.0034 < threshold=0.0050)     I highly appreciate an explanation for the meaning of this error and how to fix it.     Best John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] recon all

Thank you very much Doug, Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience !   Bests, John   Sent: Friday, November 11, 2016 at 4:42 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu S

[Freesurfer] dtrecon

/dwi.nii I re-run the same previous comand line under freesurfer 6 and the nalysis went fine.   The problem is that all my recons are prepared under freesurfer 5.3. If I use dt_recon under FS6 does this affect the results?   Thank you for any advice you provide!   Bests, John

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Thank you very much Doug. You are so awsome :)   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, November 14, 2016 at 1

[Freesurfer] Re: surface based analysis for subcortical structures

sions in the cortical parcellates vs lesions in the white matter parcellates) using the same projection factor? Or I need to change the projection factor to include more deeper structures in the analysis?   Thank you for any advice! John   Sent: Monday, November 14, 2016 at 1:29 PM From: 

[Freesurfer] surface based analysis (projfrac)

losum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ?   Thank you for any adv

Re: [Freesurfer] surface based analysis (projfrac)

ial and white. When the analysis is not showing any differne between the groups for "projfrac 0.5" and showing differnce for "projfrac 0" that means the differnce between the groups is deeper and closer to white matter. Is this correct?   Thank you for any input and clarification! 

Re: [Freesurfer] surface based analysis (projfrac)

0 , 1, 2 ", In other words, less than zero means the surface based analysis is running at a lower level of the white matter. Can the issue of the partial volume effect be avoided by using larger numbers for "projfrac" ?   Bests, John      Sent: Thursday, January 12, 2017 at 5:08

Re: [Freesurfer] surface based analysis (projfrac)

Thank you very much Doug, Kindly, do you suggest me any steps to avoid patial volume effects in surface based analyses ?   Best, John    Sent: Friday, January 13, 2017 at 12:21 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface base

Re: [Freesurfer] surface based analysis (projfrac)

between the groups in specific areas at "cwp 0.01".  How can I check that this differnce is a real differnce and not related to partial volume effect? Best, John    Sent: Friday, January 13, 2017 at 2:46 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject:

Re: [Freesurfer] surface based analysis (projfrac)

Thank you Doug for the advice , I will follow your pipeline, I see that the command  "gtmseg " is part of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ?   Best, John Sent: Friday, January 13, 2017 at 3:16 PM From: "Douglas N Greve" To: freesurfer

[Freesurfer] RAS to MNI coordinate conversion function?

rom recon-all that I'm assuming both Freeview and TkMedit use, but I can't seem to find it? Any help would be appreciated. Thanks again! Best, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of C

[Freesurfer] Tracula Tracts density

words the number of distinct tracts that pass through the manually constructed sets of ROIs) ?     Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603

[Freesurfer] recon-all stripped brains

Dear experts, I want to run recon-all on a stripped brains ( T1 images after applying bet tool). Do I need to add any flags to the command recon -all -all subjid       Bests, John   ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] MPRAGE SNR

Dear Experts, Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it.   I highly appreciate your help!   Bests, John Anderson Senior Research Associate Psychological and

Re: [Freesurfer] MPRAGE SNR

Dear Jürgen This really helps! I highly appreciate your input on this.   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent

Re: [Freesurfer] MPRAGE SNR

ted by the binary "mri_cnr"?     Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, October 19, 2015 at 8:36 AM From

Re: [Freesurfer] MPRAGE SNR

Hi All, Thank you very much for your comments!   Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it make sence ?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences

Re: [Freesurfer] MPRAGE SNR

ality of the image is fine. Also calculating the SNR, CNR want help a lot!   any suggestions?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646

[Freesurfer] Head circumference

Dear FS experts, I want to inquire if there is any script in Freesurfer that can help to calculate the head circumference from MPRAGE ? Thanks for any advice!       Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman

[Freesurfer] Head circumference

Dear FS experts, I want to inquire if there is any tool or method in Freesurfer that can help to calculate the head circumference from MPRAGE ? Thanks for any advice!       Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Voxel based vs surface based

      Bests, John    ___ 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

[Freesurfer] recon-all

differnt? (i.e In norm.mgz the voxel dimentions are equal while in orig.mgz it is not)? 3. Is it correct if I convert norm.mgz to "nii" file and use it as a "T1" for further processing?   bests, John Anderson   ___ Freesurfer

Re: [Freesurfer] recon-all

           3.5 I use reversed matrix to move the mask to FA map.   The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps?   Bests, John Anderson Senior

Re: [Freesurfer] recon-all

at it failed because the fov is more than 320 and it says that I need to run recon -all with the flag -cw256.   How can the fov affect the segmentation? in other words is it better to run recon-all on a file with fov less than 256 or more than 256 ? what is the difference in the final outpu

Re: [Freesurfer] Qdec visualization

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?   Bests, John      Sent: Monday, December 21, 2015 at 11:43 AM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization The

Re: [Freesurfer] Qdec visualization

Hi Doug, Given that the  standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation? I tried:  mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong?  

Re: [Freesurfer] Qdec visualization

nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense) On 12/21/2015 02:38 PM, John An

[Freesurfer] Integrating planes into a single volume?

Is there any way to integrate the information from axial, coronal and sagittal views into a single volume? I'm looking for ways to build a more accurate/comprehensive 3d model and I'm not having any luck finding workflows or tools that allow any sort of cross-plane refinement/interpolation. Any s

[Freesurfer] Longitudinal data analysis

upport!     Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer

[Freesurfer] Longitudinal data analysis

h esame order of the groups in qdec tables?  4. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly?   Thanks for your support!     Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Mo

[Freesurfer] P files

Dear Freesurfer experts, I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs     Thanks for any advice!   Bests, John    ___ Freesurfer mailing list Freesurfer

[Freesurfer] transform statistical map in MNI to surface

Hi Experts, I have statistical map in MNI space and I want to view it using tksurfer how can i transform this map to a surface ?     Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] transform statistical map in MNI to surface

Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis   Bests, John    Sent: Friday, January 08, 2016 at 1:41 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] transform stati

Re: [Freesurfer] transform statistical map in MNI to surface

Thanks Bruce,  if my statistical map "stat1.nii.gz"  is in MNI152 standard space what are the command lines that I need ( or if possible any link to wiki) Thanks a lot!     John  Sent: Friday, January 08, 2016 at 2:49 PM From: "Bruce Fischl" To: "Freesurfer s

[Freesurfer] Cortical thickness parcellates

Dear experts, I am wondering if there is any way to divide the cortical thickness parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate any suggestion.   Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Cortical thickness parcellates

cortical thickness by lobe?         Sent: Wednesday, January 13, 2016 at 12:41 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical thickness parcellates Try mris_divide_parcellation On 01/13/2016 12:18 PM, John Anderson wrote: > Dear ex

[Freesurfer] Longitudinal analysis_covariates

advice!   Bests, John  ___ 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

[Freesurfer] register image to mni152

  Dear experts, I wanted to register T1 mprage image to the standard space MNI152. The output of FLIRT at dof 12 is not effective. How can I get better results using bbregister? What are the commands that I need to use ?   thanks for any help! John

Re: [Freesurfer] transform statistical map in MNI to surface

ros of doing or not doing these steps?   Thanks a lot! John      Sent: Friday, January 08, 2016 at 2:57 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] transform statistical map in MNI to surface Hi John you would run recon-all on the MNI 152 T

[Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

, please let me know what and where to upload. Thanks very much for your help. Best regards, John Plass ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-m

Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

to have some of the dimensions swapped. Any idea why this might be? Thanks for your help! John On Tuesday, January 26, 2016, Bruce Fischl wrote: > Hi John > > does it come up in the correct orientation in freeview? If you didn't > scan it in the orientation that a person woul

Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

there a chance that this is affecting the later surface registration? Thanks so much for any help you can provide. I've attached mri_info output for the nifti and mgz files below. Best regards, John mri_info mprage.nii.gz Volume information for mprage.nii.gz type: nii dimens

[Freesurfer] Longitudinal analysis--mass univariate

one group of patients. The example In wiki was for four groups. 2. Can I do a comparison in cortical thickness over time between controls ( who have  only one time point ) and patients using mass univariate approach.   Bests, John  ___ Freesurfer mailing

Re: [Freesurfer] Longitudinal analysis--mass univariate

patients some also some scanned three times and some four times the rest at least two times.   Is LME -- mas usnivariate still workable with out a bias ?     Bests, John    Sent: Thursday, January 28, 2016 at 6:51 AM From: "Martin Reuter" To: "Freesurfer support lis

Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

?     Bests, John    Sent: Saturday, January 30, 2016 at 5:51 AM From: "Martin Reuter" To: "Freesurfer support list" Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed} Hi John,   What I mean is there could be a bias in your study design if 99% of group

[Freesurfer] getting vertex-wise correspondences across subjects

ould you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics Unive

[Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04 As always, I'm very grateful for any help you can provide. John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

axes swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of the volume, but the outline of an axial slice of the surface, with the anterior part pointing down. John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

that the surface registration is starting with the surface misoriented like it is in tkmedit. John --- John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University On Tue, Mar 1, 2016 at 7:38 AM, Bruce Fischl wrote: > Hi John > > this is prett

[Freesurfer] Qdec-statistical map

every subject (depending on the order of subjects in Qdec table) from this statistical map ?   Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] Qdec-statistical map

Hi Doug, How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject?   Bests, John    Sent: Thursday, March 03, 2016 at 12:37 PM From: "Douglas N Greve" To: 

Re: [Freesurfer] Qdec-statistical map

This si Great!!! Thanks Doug. One more question: What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?     Bests, John    Sent: Thursday, March 03, 2016 at 12:47 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: R

[Freesurfer] FS 6

Dear fs experts, Is there a version of fs 6 for Windows to download. Thank u John On Tuesday, March 8, 2016, Bruce Fischl wrote: > Hi David > > I'm pretty sure that the Wash U HCP group has sorted this out. Have you > asked them? > > cheers > Bruce > > > On

[Freesurfer] mri_glmfit

group1 Class group2 Input 001 group1 Input 002 group1 Input 003 group1 Input 004  group1 . . . Input C001 group2 Input C002 group2 Input C003 group2 Input C004 group2 . . .   please what I am doing wrong?! Bests, John  ___ Freesurfer mailing

[Freesurfer] FA maps surface based analysis

Hi FS experts, How can ai do surface based analysis on FA maps. In other wods: I have 20 subjects( two groups 10/10) and FA map for every subject. How can I dtufy the differnce between the groups in FA on surface?   Best, John ___ Freesurfer mailing

[Freesurfer] mri_glmfit-sim

/cortex/fwhm35/pos/th30/mc-z.csd   Thanks you for any suggestion!     Bests, John  ___ 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] Fw: mri_glmfit-sim

/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd   Thanks you for any suggestion!     Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

[Freesurfer] voxel vs surface based morphometric analysis

appreciate if you clarify that to me.     Bests, John ___ 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

[Freesurfer] mri_glmfit

    Bests, John  ___ 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

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