Re: [Freesurfer] Extraction of segmentation maps using mri_extract_label

FYI, these numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt On 1/7/15 9:19 AM, Bruce Fischl wrote: for left and right: 1. 2 and 42 2. 3 and 42 3. 10 and 49 4. 77/78/79 5. 11 and 50 6. 12 and 51 7. 13 and 52 8. We don't have a single one for all of cingulate and it depends on which parc

Re: [Freesurfer] recon-all error

That probably is not a problem since dicoms don't have to have a certain extension. To test, try running mri_convert 4571157 test.mgh To run this you must be in the folder where 4571157 is located On 1/13/15 2:14 AM, Borzello, Mia wrote: Hi Bruce, Thanks for e-mail. I did a search on

Re: [Freesurfer] R: Fwd: fcseed-sess - segmentation fault

Have you run fcseed-sess -s sessionid -cfg mean.L_Thalamus.config That is what will create that file On 1/13/15 6:50 PM, std...@virgilio.it wrote: Hi list I'm running preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run fcseed-config -segid 10 -fcname L_Thal

Re: [Freesurfer] FreeSurferOutputVolume

Try this instead mri_label2vol --seg ${mgz_file} --temp 001.nii --regheader ${mgz_file} --o ${cut1}.nii On 1/13/15 3:22 PM, Zhuang, Xiaowei wrote: Hi, I am a new user of freesurfer, mainly for hippocampus segmentation. The output of my command: recon-all -i ${subject}.nii -subject ${s

Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area

The computation is pretty simple, it is just the average of the area of the surrounding triangle. Is that what you mean or do you mean the mapping of said area to the average space? doug On 1/15/15 11:37 PM, Bronwyn Overs wrote: Dear Mailing List, I would like to understand how freesurfer

Re: [Freesurfer] vertex-wise covariate for gyrification index

That's fine. mri_glmfit-sim has a little anxiety when it finds mri_glmfit options it does not recognize. doug On 1/26/15 5:00 PM, angela.fav...@unipd.it wrote: > Hi Doug, > thank you for this hint. > I have included --pvr in my mri_glmfit command using a stack of cortical > thickness maps of the

Re: [Freesurfer] extracting pvalues

what do you mean? Just a list of values? the column, row, slice as well? On 1/26/15 4:02 PM, Hirsch, Gabriella wrote: Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having troubl

Re: [Freesurfer] Extract mean time series from parcellated region

what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s -

Re: [Freesurfer] Extract mean time series from parcellated region

ies x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka *From:* Douglas Greve *To:* sabin khadka ; Freesurfer Support List *Sent:* Monday, January 26, 2015 5:33 PM *Subject:* Re: [Frees

Re: [Freesurfer] Converting dicom images to nifti

Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not gi

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote: Hello --- I'm trying to extract quantitative T2 values for different brain segments. I've converted my T2 set of DICOMs to .mgz format using mri_convert and loaded them into freeview. >> mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

First off, I would use --init-header instead of --init-spm. Probably won't make a difference, but it is safer in this case. Second, look at the registration in tkregister (bbregister prints out the command line, you can just cut and paste). doug ps. Please remember to post the list instead o

Re: [Freesurfer] Converting dicom images to nifti

If you run it with --help there will be lots of documentation and examples. It will not be able to convert the multiframe dicom files though On 1/27/15 12:24 PM, pradeep mahato wrote: Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, "Douglas

Re: [Freesurfer] Extract mean time series from parcellated region

. I appreciate your help!! Cheers, Sabin Khadka *From:* Douglas Greve *To:* sabin khadka ; Freesurfer support list *Sent:* Tuesday, January 27, 2015 10:31 AM *Subject:* Re: [Freesurfer] Extract mean time series from

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

replies, — Noam On Jan 27, 2015, at 6:02 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote: First off, I would use --init-header instead of --init-spm. Probably won't make a difference, but it is safer in this case. Second, look at the registration in tkregister (bbreg

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

. 4000. It’s indeed encouraging that using the erode option decreases the STD, but I’m still wondering whether there a way to validate accuracy of the values. Thanks! Noam On Jan 27, 2015, at 6:50 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote: On 1/27/15 12:38 P

Re: [Freesurfer] retinotopy in subject volumetric space

ate directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

4 46 1799917999.0 Right-Cerebellum-White-Matter 6.079888.1490 0. 4000. 4000. It’s indeed encouraging that using the erode option decreases the STD, but I’m still wondering whether there a way to validate accuracy of the values. Thanks! Noam On Jan 27, 2015, at

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

file.mgz -seg aparc+aseg.mgz Thanks! — Noam On Jan 27, 2015, at 7:30 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: It is finding 0s in the T2 (the range is 0-4000). I'm not sure about the 4000, but the 0s indicate that something is strange with that image. How was it cr

Re: [Freesurfer] missing raw.fsnr files

I have no idea what the problem is. You can have it exclude the fsnr maps by adding -no-anamaps, though there might be something else going on with the data. Can you give me the location of your data and SUBJECTS_DIR as well as the command line you ran and the full terminal output of the comma

Re: [Freesurfer] average values per cluster

You should report the clusterwise p-value. The p-value that you have computed is not interpretable. If it did not come out significant, then it would be worrisome, but it is only a check and cannot be used for anything. What p-value did you get from SPSS? I'd be curious to know what the sourc

Re: [Freesurfer] Mri_segstats

There is not a flag to control the printing format. However, you can multiply the values by a constant (--mul flag). Eg, you can multiply all values by 100 or divide by 100. doug On 1/30/15 11:42 AM, Alshikho, Mohamad J. wrote: > Dear FS Experts, > In order to generate the statistics using mri_

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

Can you run the following cmd and send me the terminal output? mkcontrast -debug -anadir RM_hard_easy_fake_error -wcond 1. -.5000 -.5000 0 -sumconds -o RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave On 1/30/15 12:15 PM, Kar

Re: [Freesurfer] average values per cluster

>>>I told him it the model is a GLM with age, gender and state as covariates This is not a sufficient description. Several design matrices could be derived from this description. On 1/30/15 11:58 AM, maaike rive wrote: The p value from SPSS is 0.156. I checked with a statistician, just to be

Re: [Freesurfer] average values per cluster

It depends on the actual covariates and whether you used DOSS or DODS. The default is DODS, which is a full interaction model. Assuming that state is a categorical variable with 2 levels, you'd have 4 regressors (gender by state) + 4 more regressors (gender by state by age). If the SPSS model

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

sorry, can you send me your mkanalysis-sess command line as well? You can find it in the analysis.info file in the analysis folder On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote: > > Dear all, > > We are trying to make a new contrast for our GLM analysis, however we have > the following fl

Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

The sudo is causing it to run under a different user (root) which means that it opens a new shell that does not have the proper environment set. Why are you running it as root? If you set SUBJECTS_DIR to something other than /Applications/freesurfer/subjects you won't have to run as root d

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, January 30, 2015 1:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkcontrast-sess "

Re: [Freesurfer] missing raw.fsnr files

lf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, January 30, 2015 11:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing raw.fsnr files I have no idea what the problem is. You can have it exclude the fsnr maps by adding -no-anamaps, though there might be some

Re: [Freesurfer] average values per cluster

Actually, that looks correct. Is this what you fed to SPSS? On 1/30/15 2:07 PM, maaike rive wrote: Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used DODS, and assumed these were may regressors: diagn1*state1*gender1 diagn1*state1*gender2 diagn1*state2*gender1 diagn1*state2*gend

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, January 30, 2015 1:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized." sorry, I wanted the mkanalysis-sess cmd, not the mkcontrast-sess On

Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

ccess and be able to avoid using sudo, before getting this message. Any help would be greatly appreciated! On Fri, Jan 30, 2015 at 1:50 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: The sudo is causing it to run under a different user (root) which means that it

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, January 30, 2015 2:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized." &g

Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

On Fri, Jan 30, 2015 at 3:11 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Do you have write perms to this file and the folder it is in? /Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env to /Users/Tyler/Documents/freesurfer/subjects/b

Re: [Freesurfer] fscalc.fsl bad dim error

what is your command line? Can you reduce it down to a file that seems to be giving you problems? On 2/1/15 1:48 PM, Jonathan DuBois wrote: Hi Freesurfers, I am trying to use fscalc.fsl to do calculations on an fsaverage vertex map of values (mgh files). In some of these files, but not all,

Re: [Freesurfer] vertexwise statistical modeling

On 2/2/15 3:56 AM, Schweren, LJS (med) wrote: Dear freesurfer experts, I investigate case-control differences in cortical thickness in a group of 11 to 30 year olds. I ran vertex-wise analyses with glmfit, with covariates age and age-squared, to take into account confounding by age as we ha

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

First, I would run the ROI analysis in mri_glmfit to see if you get the same results as in SPSS. In the handfull of these cases, no one has been able to correctly replicate the FS design matrix in SPSS, so I suspect that is part of the discrepancy. The other thing is that ROI and vertex-wise

Re: [Freesurfer] subsampling procedure for fsaverages

you can also use mri_surf2surf to do the mapping On 2/2/15 11:38 AM, Bruce Fischl wrote: Hi Ernst The new vertices are added o the end, so all the fsaverage5 vertex numbers should be the same in fsaverage6 Cheers Bruce On Feb 2, 2015, at 10:33 AM, Ernst Schwartz

Re: [Freesurfer] Calculate the DTI metrics inside a single voxel

Hi Mohamed, that looks great, very clear. We'll have to engage your services to write some of our wiki pages :) doug On 2/2/15 1:05 PM, Alshikho, Mohamad J. wrote: Sorry for the mistake: I wanted to correlate the DTI metrics inside this single voxel with the concentration of the metabolit

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

he NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 3/02/2015 3:31 am, Douglas Greve wrote: First, I would run the ROI analysis in mri_glmfit to see if you get the same results as in SPSS. In the handfull of these cases, no one has been able to correctly replicate the FS design

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

;Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 3/02/2015 11:03 am, Douglas Greve wrote: Even easier. Run aparcstats2table, then run mri_glmfit passing the output of aparcstats2table with --table (instead of --y). There's something on the wiki ab

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 3/02/2015 2:00 pm, Douglas Greve wrote: This is not something you would run the MC sim on because there is no clustering, it is just a lis

Re: [Freesurfer] vertexwise statistical modeling

again, Lizanne *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* maandag 2 februari 2015 17:19 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] vertexwise statistical modeling On 2/2/15 3:56 AM

Re: [Freesurfer] defining ROIs/clusters

Just run mris_preproc on your healthy group, then run mri_segstats using the cluster annotation from your first analysis and the HC stack as the input. Does that make sense? doug On 2/3/15 9:18 AM, maaike rive wrote: Hi all, Does anyone know how to extract average (thickness/area/GI) value

Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

Hi Corinna, In each iteration, the mc-full replaces your data (--y) with white gaussian noise, smoothes it, then computes the GLM and p-values from the t or F-test. The mc-z ignores your data entirely and creates a single frame of WGN in each iteration, smoothes it, rescales it back to a z, t

Re: [Freesurfer] tksurfer

Is it world readable? You might also change its name to license.txt On 2/3/15 12:13 PM, André Schmidt wrote: Dear experts, I like to see the obtained annotation files using tksurfer. However, I already got the following error message if I use tksurfer HC001 lh inflated in the terminal: Fr

Re: [Freesurfer] Surface based smoothing

There are no explicit weights. It just uses an iterative procedure in which the value at a vertex is replaced by the average of itself and its neighbors. This approximates gaussian smoothing with the number of iterations being related to the FWHM. doug On 2/4/15 9:01 PM, Simon Vandekar wrote:

Re: [Freesurfer] average values per cluster

On 2/8/15 1:48 PM, maaike rive wrote: But how can i run the appropriate preprocessing and smoothing? The --X flag s not recognised using mris_preproc. mri_preproc only uses the fsgd file to get the list of subjects to assure that they are ordered in the same way as when mri_glmfit builds the X

Re: [Freesurfer] time series data from FSFAST

Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region usi

Re: [Freesurfer] time series data from FSFAST

match error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka ---- *From:* Douglas Greve *

Re: [Freesurfer] time series data from FSFAST

while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka ---- *From:* Douglas Greve *To:* freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Map volume label to surface label

If the labels are a segmentation volume, then you'll need to run mri_vol2surf with --interp nearest. doug On 2/10/15 6:39 PM, Bruce Fischl wrote: Hi Razib yes, I think mri_label2label will do this if you have reconstructed the surfaces. cheers Bruce On Tue, 10 Feb 2015, Muhammad Razib wr

Re: [Freesurfer] Help: error on running dt_recon

Just give it one of the dicoms (ie, don't use the "*" wild card, just give it the actual file name of one of the files in the series, it will find the rest) doug On 2/11/15 4:28 PM, Sampada Sinha wrote: Dear freesurfer experts, Sorry for posting such a long message but I am trying to run dt

Re: [Freesurfer] Interhemispheric registration of .mgh files

Probably easier to use mris_apply_reg, something like mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \ --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \ $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi

Re: [Freesurfer] Interhemispheric registration of .mgh files

btw, to check, you can run this on the thicknesses and compare to what you get with mris_preproc On 2/11/15 6:01 PM, Douglas Greve wrote: > Probably easier to use mris_apply_reg, something like > > mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \ > --streg $

Re: [Freesurfer] To visualize contribute of each subject in FS-FAST

I don't understand what you are trying to do. Do you want a "time" course at a voxel, i,e a plot where "time" is subject? Or do you want to visualize a map of each subject? On 2/14/15 5:31 AM, std...@virgilio.it wrote: Hi, I'm using FS-FAST for seed based connectivity analysis. I'd like to v

Re: [Freesurfer] Entorhinal Cortex segmentation and volume

On 2/16/15 9:31 AM, Bruce Fischl wrote: > Hi Melina > > 1. Can you send us a picture? I'm not sure given your description, > although the surfaces can be arbitrary in the hippocampus/amygdala and > should be ignored there. This corresponds to the "cortex unknown" label in aparc (and is probably

Re: [Freesurfer] Entorhinal Cortex segmentation and volume

t;normal" and can I trust those borders? Or would you rather advise to control aseg and aparc segmentation to estimate the entorhinal cortex segmentation? 2. You're right, Bruce, in freeview the exvivo label it just follows the surface. So I'll try mri_label2vol. Cheers Melina

Re: [Freesurfer] Map volume label to surface label

about. How can I get this registration file? Do I need to create this using freesurfer? I highly appreciate your time and suggestion. Thanks On Tue, Feb 10, 2015 at 9:54 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: If the labels are a segmentation volume, then yo

Re: [Freesurfer] fsaverage surfaces correspondence across hemispheres

We don't have anything to do this directly. However, we do have this tool: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi See if that meets your needs. doug On 2/17/15 12:49 PM, David Moreno-Dominguez wrote: > Hello, > I am performing clustering ofer data sampled to the fsaverage5 surfaces. > I

Re: [Freesurfer] Register.dof

a T1 space. Is it possible? Thanks, Xiaomin On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: We don't have anything to do this directly. However, we do have this tool: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi Se

Re: [Freesurfer] cluster colors

I don't think I understand. What files are you visualizing? What is your command to visualize? On 2/18/15 3:42 PM, Hirsch, Gabriella wrote: Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu

Re: [Freesurfer] FSFAST

On 2/18/15 4:38 PM, sabin khadka wrote: Hi FS Users- After using FSFAST's preproc-sess command (I get the output files: fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well the EPIs are mapping onto th

Re: [Freesurfer] extract individual label from Destrieux Atlas

Use --annotation a2009s.aparc On 2/19/15 8:34 PM, Yang, Daniel wrote: Dear FreeSurfer experts, The following command works but how do I get the labels from —a2009s ? mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir . What is the difference between a2005s and a2009s? Than

Re: [Freesurfer] Bad design matrix

Try demeaning your covariates. By demeaning, I mean to compute the mean across all subjects, then subtract the mean from all values (for each covariate). doug On 3/1/15 2:40 AM, Anders Hougaard wrote: Dear all, I'm comparing cortical thickness of a group of patients to a group of controls.

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Basically looks ok. The only things that jump out at me are that you are using regheader (I would create a registration file with bbregister rather than assuming that there was no motion between the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come from? doug On 2/27/15 2:16 PM

Re: [Freesurfer] regional surface area differences

regions. > > An implementation of the method we proposed in the paper is available > for Octave and/or Matlab at http://brainder.org/download/areal > It works fine, but beware that it's quite slow. > > All the best, > > Anderson > > > > 2013/5/13 Douglas Gr

Re: [Freesurfer] freeview registration

I think that freeview does not correctly generate the registration file. You can use it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18 AM, Xiaomin Yue wrote: Hi All, After using freeview to manually adjust the registration between a functional

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

On 3/3/15 9:41 AM, Sarah Finnegan wrote: > Hi Doug, > > Thanks I had hoped to use mri_mask but was foiled in my attempt to convert > the .label files to .mgz using mri_label2bvol. I assumed I must be on the > wrong track. > > my command was > > mri_label2vol --label V2_lh.label --temp f.nii.g

Re: [Freesurfer] Problems with MonteCarlo analysis

The first command sets the voxel-wise threshold to p<.0001, which is pretty strict by itself. Is that what you wanted? Do voxels survive uncorrected at that level? The 2nd sets the voxelwise threshold at about .05. In both cases the clusterwise correction is .05 (ie, neither are 0.9), so I'm

Re: [Freesurfer] selxavg3-sess error

It looks like different runs have different number of slices. Is that right? On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote: Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following:

Re: [Freesurfer] Calculating Total Brain Volume using 5.1 outputs

I think I would download a new version of mri_segstats (call it something like mri_segstats-5.3) ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch cd $SUBJECTS_DIR/subject mri_segstats --seg mri/aseg.mgz --sum stats/aseg.53.stats --pv mri/norm.mgz --empty --brainmask mri/brain

Re: [Freesurfer] selxavg3-sess error

Hamdi *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] *Sent:* Monday, March 09, 2015 2:38 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] selxavg3-sess error It looks like diff

Re: [Freesurfer] Monte Carlo Simulation

Yes, that probably is the reason. doug On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote: > To be honest, I checked the between subject alignment and it looked pretty > good. None of my subjects was way out of alignment. However, since we cannot > fit the whole brain in the slice during scan

Re: [Freesurfer] GLM analysis on CBF maps

For the intercept, you are testing for a difference in the mean CBF between the groups regressing out the effects of gender and age. For the slope, you are testing for an interaction between group and age regressing out the effects of gender. doug On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote

Re: [Freesurfer] mri_glmfit on Cortical Thickness : variable significant results with cluster threshold

It does not discredit your results. This is not unexpected behavior. As you change cluster forming thresholds, the clusters will change sizes, but the null distribution will also change in complicated ways. The end result is that it is not easy to predict the effect on the number and sig of yo

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

On 3/13/15 10:10 AM, Krieger, Donald N. wrote: > Dear List, > > Sorry to be unclear in my questions. I had a fundamental misunderstanding > which I hope to rectify. > > (1) It appears that what is called the "freesurfer" coordinate system > (tkregister) is represented by subject fsaverage. 3D

[Freesurfer] Fwd: Postdoc position in biostatistics in Copenhagen, Denmark, available

anyone interested, please contact Gitte directly doug Forwarded Message Subject: Postdoc position in biostatistics in Copenhagen, Denmark, available Date: Tue, 17 Mar 2015 14:35:36 +0100 From: Gitte Moos Knudsen To: Douglas N Greve Hi Doug Hope things are we

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

what do you mean by equidistant distance? On 3/17/15 12:54 PM, Victor Montal Blancafort wrote: Hi FS expert, I was wondering if it is possible to create multiple "circular" ROIs on a surface with equidistant distance. Since the distance between vertex is not constant, it works if the number o

Re: [Freesurfer] R: Re: isxconcat-sess problem

do you have another double dash (--s) in the command line? On 4/3/15 1:00 AM, std...@virgilio.it wrote: Thank you very much. I have resolved Sess49 (--s) error but the "ERROR: Flag —s unrecognized" is still remained. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 31-

Re: [Freesurfer] R: Re: R: Re: isxconcat-sess problem

Does Sess14 have a double dash? On 4/4/15 3:38 AM, std...@virgilio.it wrote: No, do you think that a folder is lacking (please see below)? Thanks Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 3-apr-2015 7.34 A: Ogg: Re: [Freesurfer] R: Re: isxconcat-sess problem do

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

I'm not sure what the problem is, but it occurs to me that computing the mean over the cluster is probably not what should be done. Instead, the total should be computed. In the header of that file, there should be a command line for mri_segstats. Cut and paste that into a shell and add --accum

Re: [Freesurfer] fs-fast analysis on a group averaged surface

Use the (undocumented) -trgsubject flag On 4/6/15 9:10 AM, Xiaomin Yue wrote: Hi All, I generated a group averaged surface using make_average_surface successfully. Currently, I like to process the fMRI data using this group surface, instead of fsaverage, using the fs-fast pipeline. For do

Re: [Freesurfer] Content of register.dof6.dat.param

Those numbers do not have the same interpretation as as the ones in fmc.mcdat but they represent the same information. If you construct a new file with the same format as fmc.mcdat but with those numbers substituted in cols 2-7 then you should get pretty similar results. On 4/9/15 7:04 AM, pf

Re: [Freesurfer] mri_vol2surf for 4D functional images in freesurfer space

Just use --regheader subject On 4/11/15 11:27 AM, Sabine Oligschläger wrote: Dear FreeSurfer's, A question regarding mri_vol2surf usage: I have 4D functional images that are preprocessed and already in freesurfer space. I would like to project them to the fsaverage surface template using

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

If you did the analysis in the volume, then you have to do the clusterwise correction in the volume. On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote: Dear experts, I had to make volumic statistical analysis for the need to use BPM toolbox. So, I got in the output of this statistical analysis som

Re: [Freesurfer] Content of register.dof6.dat.param

sult for the motion > regressors valid? > > > > On Mon, 13 Apr 2015 10:15:08 -0400 > Douglas Greve wrote: > >> Those numbers do not have the same interpretation as as the ones in >> fmc.mcdat but they represent the same information. If you construct a >> new f

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

How could I do ? Best regards, Matthieu 2015-04-13 16:27 GMT+02:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>: If you did the analysis in the volume, then you have to do the clusterwise correction in the volume. On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote: Dea

Re: [Freesurfer] bootstrap/jackknife in qdec?

No, sorry. doug On 4/14/15 7:28 AM, Fred Dick wrote: > Dear Doug et al., > > is there a hidden option (perchance) to get bootstrapped estimates of the > correlation coefficients/regression parameters in qdec? > > cheers > Fred > ___ > Freesurfer mailing

Re: [Freesurfer] mri_segstats_flags_more questions

On 4/14/15 9:59 AM, Alshikho, Mohamad J. wrote: Hi Doug, If I check the file "aseg.stats" ( the output of the command line recon-all –subjid –all ) I don't see in the table (in the file "aseg.stats" ) any volumes regarding right and left hemispheric white matter. It is not supposed to b

Re: [Freesurfer] dimension mismatch

Don't use the --inv flag on vol2vol doug On 4/14/15 10:03 AM, Thomas Potrusil wrote: Dear FreeSurfers! After successful registration using dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtirecon I resampled the anatomical into the functional space using (I´m interested in ADC-

Re: [Freesurfer] mri_vol2vol

sorry, I don't understand. fstal would imply that you want talairach space. If you want to map the functional into the anatomical space, then mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg register.dof6.dat --fstarg On 4/14/15 11:36 AM, Xiaomin Yue wrote: Hi Doug, I like to c

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

So BPM does not do clusterwise correction? You could use mri_volcluster, but you'll need to know the FWHM of your BPM analysis doug On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote: Dear FreeSurfer's experts, For personnal need I use the BPM toolbox (Biological Parametric Mapping) to compute GLM

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

t does the FWHM of the BPM analysis correspond to ? And how to find it ? Manu thanks ! Best regards, Matthieu Le 15 avr. 2015 00:23, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : So BPM does not do clusterwise correction? You could use mri_volcluster

Re: [Freesurfer] mri_vol2vol

So you want it to be in a volume with field of view 256mm in all three dimensions, but the voxel size to be that of the functional data? It is possible to do, but not easy to set up. Can you say why you would want to do that? On 4/14/15 8:20 PM, Xiaomin Yue wrote: Thanks for your response.

Re: [Freesurfer] Why weighted least squares?

In theory, WLS is the optimal estimator in the case where variance differs across subject. The FS implementation actually computes "psuedo-WLS" in which the weights are just the inverse of the first level variance. A true WLS would use the random effect variance plus the lower level variance. T

Re: [Freesurfer] mri_vol2vol

But why do you need to have the same resolution as the original functional? On 4/14/15 10:30 PM, Xiaomin Yue wrote: yes, that's precisely what I want. the reason is the following. A subject was scanned multiple times across days with slightly different slice position for each time. What I ne

Re: [Freesurfer] dimension mismatch

resampling the anat to funct space... Visual inspection of data showed that registration is very good but scrolling through adc map with aseg-overlay revealed these PVEs... Thanks, Tom *Gesendet:* Mittwoch, 15. April 2015 um 00:19 Uhr *Von:* "Douglas Greve" *An:* freesurfer@nmr.mgh.h

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

in this case you said I need to know the FWHM of my BPM analysis, how could I obtain this ? --> Would I have access in this way to arguments --cache and --cwp as used in mri_glmfit-sim ? I hope I have been clearly. Thanks in advance for guiding me ! Best regards, Matthieu 2

Re: [Freesurfer] Exporting Qdec Data

try mri_segstats --i y.mgh --vox vertexno 33 0 0 --avgwf out.dat On 4/15/15 6:41 PM, Lindsay Renae Wessel wrote: > Thanks! I now get the following error: > > "ERROR: Option out.dat unknown" > > The exact command I have entered (for vertex 33) is: > > "mri_segstats --i y.mgh --vox vertexno 33 --a

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