[Freesurfer] mri_volsynth

Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space.   mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii     I ha

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

[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

ar subvolumes. cheers Bruce On Wed, 8 Jun 2016, John Anderson wrote: > 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 ) > Than

Re: [Freesurfer] Break 3D volume

g box, and (dx,dy,dz) is the extent of it (in voxels) On Wed, 8 Jun 2016, John Anderson wrote: > Hi Bruce,  > Thank you for the quick response. it is really highly appreciated! > I have 3D mask in the form of nifti file and it has the shape of large > square( the black big square in my

[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! Bests, John ___

[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

Hello, FS experts, I am trying to use QA tool:  I ran the following command  recon_checker -snaps-only -s-file subjects.txt   The script output the following: X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0 X1

[Freesurfer] Volume or surface?

Dear FS experts, I want to know what is the output (volume or surface) of the following scripts. (The input is file.nii.gz which is a volumetric ) 1. spmregister --s subj --mov file.nii.gz --reg reg.dat --o file_t1.mgh #is the output file (file_t1.mgh) is a volume or a surface    2. mris_prepr

[Freesurfer] surface based analysis for subcortical structures

Dear experts, I ran surface based analysis using PET maps. As the following:   spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh mri_surf2sur

[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/free

Re: [Freesurfer] surface based analysis for subcortical structures

On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_

[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

y 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 subc.glmdir --cache 1.3 pos --cwp 0

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

Dear Freesurfer experts, I ran the following command on a T1 image recon-all -subjid 089 -all -qcache   and I got the following error message:   talairach_afd -T 0.005 -xfm transforms/talairach.xfm   ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0344

Re: [Freesurfer] recon all

I'm afraid that it might left-right rev the volume. In either case, you can manually check the tal reg to see if it looks ok. On 11/11/2016 03:56 PM, John Anderson wrote: > Thank you Doug, > Attched are to snapshots > #1 is for the original T1 ( i.e. as aquired) and this image wh

[Freesurfer] dtrecon

Dear Freesurfer experts, I want to analyze DTI data using the command  dt_recon --i dwi.nii --b bvals bvecs --s subj1 --o /subj1   Under Fressurfer 5.3, the analysis fail showing this error message: nifti1Read(): unsupported slice timing pattern 5 in /data/anaconda/mesgp/dtrecon3/subj1/dwi.nii

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

"John Anderson" To: freesurfer@nmr.mgh.harvard.edu Subject: 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,

[Freesurfer] surface based analysis (projfrac)

Dear FS experts, I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"   I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get t

Re: [Freesurfer] surface based analysis (projfrac)

cortical GM. If you mean in GM near the CC, then the analysis is appropriate. The projfrac parameter sets the sampling location between the white and pial surfaces where 0.5 means half way.   On 1/10/17 8:07 AM, John Anderson wrote: Dear FS experts, I am working on surface based analysis using frees

Re: [Freesurfer] surface based analysis (projfrac)

PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) yes, that is correct. However, understand that there might only be a difference of 1mm between those two locations, so it could easily be a partial volume effect On

Re: [Freesurfer] surface based analysis (projfrac)

d analysis (projfrac) On 01/12/2017 05:20 PM, John Anderson wrote: > Thank you very much Doug and thank you for briniging the issue of > "partial volume effect " to my attention. Kindly, I have one last > question. > I found in wiki that the default values for projfrc value

Re: [Freesurfer] surface based analysis (projfrac)

 Re: [Freesurfer] surface based analysis (projfrac) What is the modality you are looking at? On 01/13/2017 02:08 PM, John Anderson wrote: > Thank you very much Doug, > Kindly, do you suggest me any steps to avoid patial volume effects in > surface based analyses ? > Best, > John > *Se

Re: [Freesurfer] surface based analysis (projfrac)

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) These differences are hard to track down because they are so subtle. You may want to use our PET module, which includes PVC http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer On 01/13/2017 03:10 PM, John Anderson wrot

[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 https

[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 htt

[Freesurfer] Voxel based vs surface based

Hi Doug and Bruce, Kindly, I have question regarding the difference between voxel based ( VBM/ FSL pipeline) and surface based analysis ( Freesurfer ).   I have two groups of subjects Group A and Group B I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to check the differenc

[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

freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all   On 11/5/15 8:37 AM, John Anderson wrote: Thanks a lot Doug! Kindly  ... 1. What do you mean by intensity normalized? Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coil

Re: [Freesurfer] Qdec visualization

correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number. On 12/18/2015 03:17 PM, John Anderson wrote: > Hi Freesurfer experts, > I am using Qdec in Freesurfer 5.3 to do some cortical thickness > comp

Re: [Freesurfer] Qdec visualization

andard variance (so take the square root) On 12/21/2015 02:08 PM, John Anderson wrote: > 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:

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] 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@nmr.m

[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/list

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

stical map in MNI to surface If it is in mni152 space, then you can run recon-all on the mni152 T1 map, then use mri_vol2surf with --regheader to map the volume tothe surface, then use tksurfer or freeview to view the resulting map On 01/08/2016 12:49 PM, John Anderson wrote: > Hi Expe

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

upport list" Subject: Re: [Freesurfer] transform statistical map in MNI to surface you wouldn't run it on the stats map - you would run it on the T1-weighted MNI152 volume On Fri, 8 Jan 2016, John Anderson wrote: > Thanks you Doug, > Kindly how can I run recon-all on the statistica

[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.edu https://

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

Dear Dr Martin, I have longitudinal database for subjects scanned multiple times. I want to study the changes in cortical thickness over time. I prepared my longitudinal table  ( column#1 fsid column#2 fsid-base column#3 group column#4 bilateral motor cortex thickness column#5 time (years) column#

[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

1 image (NOT your map), then use mri_vol2surf to map the stats map onto the resulting surfaces. Note that this won't give you great results as a bunch of your clusters will probably not be near the cortical surface (since in general subjects cortices don't align well in MNI 152) cheers B

[Freesurfer] Longitudinal analysis--mass univariate

Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have only one time point.   I aim to : 1. I wanted to study the changes in cortical thickness over time in e

Re: [Freesurfer] Longitudinal analysis--mass univariate

t, Martin     On Jan 28, 2016, at 12:23 PM, John Anderson <j.ander...@publicist.com> wrote:   Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have

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

ditional co-variates in your LME model.    Best, Martin   On Jan 28, 2016, at 1:12 PM, John Anderson <j.ander...@publicist.com> wrote:   Thanks a lot D martin for your quick answer. Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Gr

[Freesurfer] Qdec-statistical map

Dear FS experts, I am using Qdec to study the differnce in cortical thicnkess between two groups. Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess. How can I extract the numbers of cortical thickness for every

Re: [Freesurfer] Qdec-statistical map

freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-statistical map not sure what you mean. the statistical map will have a single value, not a value for each subject On 03/03/2016 12:31 PM, John Anderson wrote: > Dear FS experts, > I am using Qdec to study the differnce in cortical thicnke

Re: [Freesurfer] Qdec-statistical map

a row for each frame in y.mgh (ie, each subject) and a column for each cluster On 03/03/2016 12:43 PM, John Anderson wrote: > 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 > betw

[Freesurfer] mri_glmfit

Hi FS experts, I am trying to run OSGM analysis between two groups using mri_glmfit as follow : mri_glmfit --y lh_10mm.mgh --fsgd fsgd.dat --glmdir lh_10mm --surf fsaverage lh --osgm    it keep returning as: ERROR: DOF = 0   my FSGD is as follow  GroupDescriptorFile 1 Title OSGM Class group1

[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 l

[Freesurfer] mri_glmfit-sim

Hi experts, I am trying to correct the results of groups analysis using mri_glmfit-sim the command is : mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166 I receive the follwoing error :   ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cort

[Freesurfer] Fw: mri_glmfit-sim

  Hi FS experts, I am trying to correct the results of groups analysis using mri_glmfit-sim the command is :   mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166   I receive the follwoing error :   ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/

[Freesurfer] voxel vs surface based morphometric analysis

Hi Doug, I ran voxel based analysis in FSL to check the differnce in PET signal between two groups. The results are totally differnt than surface based analysis in Freesurfer.  I this real or I am doing something wrong? I tried to do the same but using FA maps and also I got totally differnt resul

[Freesurfer] mri_glmfit

Hi Experts, What is the meaning of this error as an output of the command mri_glmfit   Found 0 voxels in mask ERROR: no voxels found in the mask   make sure at least one voxel has a non-zero value for each input   in other words what are therrors that can lead to such like error message    

Re: [Freesurfer] tksurfer

cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI   On 3/16/16 9:43 AM, John Anderson wrote: Dear experts, I am running into

[Freesurfer] mri_fwhm

Hi FS experts, I am trying to use the folowing command:  mri_fwhm --i lh.mgh --auto-mask 0.2 --sum lh.fwhm5.sum --fwhm 5 --o lh_5mm.mgh   I keep receiving an error message as follow:   voxelvolume 1 mm3 Computing mask, relative threshold = 0.2, gmean = 0.501858, absthresh = 0.100372 Search re

[Freesurfer] longitudinal data analysis

Hi Dr Martin I want to study the change in cortical thickness overtime in one group of subjects. I have only one group of subjects who scanned multiple times ( two time points and more) I followed the pipeline exactly as in wiki. I want to inquire about  X in this case . Is it supposed to be 1

Re: [Freesurfer] longitudinal data analysis

03/21/2016 12:40 PM, John Anderson wrote: Hi Dr Martin I want to study the change in cortical thickness overtime in one group of subjects. I have only one group of subjects who scanned multiple times ( two time points and more) I followed the pipeline exactly as in wiki. I want to inquire abo

[Freesurfer] V1 Atlas ( brodman maps)

Dear experts,  I want to use the atlas V1 to calculate PET signal for Brodman areas. How can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all the BAs in one file) to feed it in the command “mri-segstat”? Bests, John  ___ Freesur

Re: [Freesurfer] V1 Atlas ( brodman maps)

uot; Subject: Re: [Freesurfer] V1 Atlas ( brodman maps) Hi John recon-all should create lh.BA.annot and rh.BA.annot parcellations that contain all the Brodmann areas we know how to label cheers Bruce On Thu, 12 May 2016, John Anderson wrote: > Dear experts, >  I want to use the atlas V

[Freesurfer] V1 Atlas ( brodman maps)

Dear Experts, I want to calculate PET signal within each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the brain I do the following:   bbregister  --t1 --mov T1_MPRAGE.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID    mri_vol2vo

[Freesurfer] surface based analysis

Hello Freesurfers, I am working on a PET surface based analysis between two groups. I did the following: 1. I concatentaed the PET images  using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere. 2. I smoothed "lh.mgh and rh.mgh) using

Re: [Freesurfer] surface based analysis

. You'll have to build your own. here are the instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 01/26/2017 01:09 PM, John Anderson wrote: > Hello Freesurfers, > I am working on a PET surface based analysis between two groups. I did > the following: > 1.

[Freesurfer] bbregister

Hi FS experts, I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command  bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj   do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images?   Best,

[Freesurfer] Fw: Re: bbregister

e. I guess it might make the initialization less robust, not sure, but I expect it works pretty well without doing brain extraction cheers Bruce On Fri, 10 Feb 2017, John Anderson wrote: > Hi FS experts, > I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using > th

[Freesurfer] bbregister

volume. I guess it might make the initialization less robust, not sure, but I expect it works pretty well without doing brain extraction cheers Bruce On Fri, 10 Feb 2017, John Anderson wrote: > Hi FS experts, > I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using >

[Freesurfer] mri_segstats

Dear Freesurfer experts, I have used the following commandline to generate the final statistics in my analysis: mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum stats.dat The final output of this command is (attached). Depedning on the anatomical location of the ma

[Freesurfer] bbregister vs spmregister vs mri_coreg

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differe

Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

. bbregister uses the BBR cost function and is preferred for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote: Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemen

[Freesurfer] Reslice image

Dear experts: I have nifti file with 96 slices. I want to re-slice it to form nifti file with 200 slice. Are there any tools in Freesurfer that can help to achieve this? Many thanks for any suggestion John___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] Moving fa map from talairach to MNI

Hi Freesurfer experts, I followed "dt_recon" pipeline https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon to analyze DTI data. The analysis ran smoothly without any issues. I want to inquire waht is the correct method to move "fa-tal.nii" to MNI152_2mm Is this command correct"? mri_vol2vol --mov f

Re: [Freesurfer] FW: MPRAGE images dimension different {Disarmed}

Dear Dhaval, when your recon-all finishs the process you will get images 256^3 and 1mm isootropic. The you can simply follow the instructions mentioned here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your images back to native space. All the best, John > > On Mon,

[Freesurfer] Volume vs cortical thickness

Dear Freesurfer experts, I highly appreciate if anybody clarify how Freesurfer calculate cortical thickness and gray matter volume. If the cortical thickness of e.g. precentral gurus is measured as the closest distance from the gray-white boundary to the gray-CSF boundray at each vertex on the t

Re: [Freesurfer] manual edits

17 11:04 AM UTC Time: April 12, 2017 3:04 PM From: seman...@nyspi.columbia.edu To: John Anderson , freesurfer@nmr.mgh.harvard.edu Hi John, Yes understanding how freesurfer deals with edits can be a bit confusing. I have a lot of experience doing edits to the wm.mgz and brainmask.mgz for

[Freesurfer] White matter atrophy

Dear Freesurfer experts, I know how to do cortical thickness group analysis using Freesurfer, also I know how to use Qdec to compare groups regarding gray matter volume differences, cortical thickness, curvatures, area,... etc. I am wondering if there is any way in Freesurfer to study the differe

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