Re: [Freesurfer] Surface-based Interhemispheric Registration : Compare left vs. right patients

Best regards, Matthieu Le 21 août 2015 19:49, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : Sorry, what is the problem? Is sounds like xhemi should be apprpriate for your application. fsaverage is not symmetric and will lead to biased results.

Re: [Freesurfer] check Talairach registration using Freeview

Koene, can you give the full command line and the full terminal output? I can't remember what was in your previous email (and I've deleted it:) doug On 8/21/15 5:20 PM, Koene Van Dijk wrote: > actually the error in the command line window is: > "Not reading in xfm fileinfo" > > > > > > > > > ___

Re: [Freesurfer] hello freesurfer developer~

On 8/25/15 9:35 AM, A-reum Min wrote: Hello developers I have some question to you. 1.In fig.png, how many vertices were composed of cluster at least? I'm not sure what you mean. it does not look like there are any clusters there 2. How to change Area Threshold(fig.png)? The area is contro

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

Run recon-all -aparc2aseg On 8/24/15 7:00 PM, fmri wrote: Hello FreeSurfer, How do I get edits made on aseg.mgz to reflect onto the aparc+aseg.mgz? I have tried the *recon-all -autorecon2-noaseg -subjid mysubject* * * but the aparc+aseg.

Re: [Freesurfer] Create matrix

does mri_volsynth not work for this? On 8/26/15 9:25 AM, Alshikho, Mohamad J. wrote: Hi Doug, I am using the command “mri_volsynth” to create voxel has specific dimensions and position in the brain. Kindly, I would like to inquire if there is any tool in Freesurfer that can help to create

Re: [Freesurfer] Create matrix

ide > this big volume into smaller voxels ? > > > Thanks! > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesda

Re: [Freesurfer] Create matrix

olume! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, August 26, 2015 10:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Create matrix No pic att

Re: [Freesurfer] making ROI after bbregister

I'm not sure what you mean. bbregister does not divide gm into layers. Can you elaborate on what you have done and trying to do? On 8/26/15 11:02 AM, Yun Wang wrote: > Dear all experts, > > > I am currently dividing the gray matter into 6 different layers using > bbregister, however, does anyone

Re: [Freesurfer] Doss/Dods

it looks like you have the correct design. I would look for an interaction between group and age (contrast 0 0 1 -1) in the dods model. If there is none, then go to a doss model with 1 -1 0 contrast. If there is an interaction, then some say you cannot test for a simple difference in the groups

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

On 8/27/15 1:13 PM, Francesco Puccettone wrote: Hello all, I have seen several (older) papers that draw conclusions about the implication of a brain region in a given task by using the following logic: region X was activated in the contrast /taskA>baseline/, but not in the contrast /taskB>b

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

On 8/27/15 1:20 PM, Francesco Puccettone wrote: Sorry, forgot to add one additional (related) question: is it ever correct to say "for region Y, the activations found for taskA were smaller than for taskB" just based on the two contrasts /taskA>baseline /and /taskB>baseline/? Or is it necess

Re: [Freesurfer] Fw: Did not find any volume geometry information in the surface

You can ignore that warning. It has been fixed in the next version. On 8/28/15 3:25 AM, car...@van-vlodrop.de wrote: *Gesendet:* Sonntag, 23. August 2015 um 17:06 Uhr *Von:* "car...@van-vlodrop.de" *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Did not find any volume geometry information in t

Re: [Freesurfer] Magnitude of group difference

There are a couple of things you can do. You can create a contrast for each group separately, then compute the voxel-wise percent difference between the maps, eg, fscalc group1/gamma.mgh pctdiff group2/gamma.mgh -o pctdiff.mgh You can compute the percent differences from the average in the

Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

what is your command line? Can you run it without the annotation? On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote: Dear Freesurfer experts, It seems impossible to load ?h.aparc.annot annotation file on ?h.pial surface of the fsaverage_sym subject. When I try under freeview, it crashes and gives

Re: [Freesurfer] F test results

Of *Douglas Greve *Sent:* 21 August 2015 19:07 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] F test results You need to use 1 -1 0 0 1 0 -1 0 On 8/19/15 11:38 AM, Lim, Lena wrote: Dear experts, I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a

Re: [Freesurfer] Non-matching results for area ROI group analysis using two different approaches

1) Why is there a difference between the 2 methods for area but not thickness ? Area needs a jacobian correction and thickness does not 2) What is the 'correct' method for area (if any) ? Or is there a better method for an ROI analysis of area? If you are going to use mri_surf2surf, then add

Re: [Freesurfer] Monte Carlo correction

No, QDEC is a very limited tool. You'll have to use the command line (mri_glmfit-sim). Also, you'll need to register each of your subjects to the new atlas (surfreg), then specify the average subject AND the new registration when running mris_preproc to create a new y.mgh file. None of this can

Re: [Freesurfer] Missing clusters in Qdec

it might be. Try lowering the threshold to see if the other clusters appear On 8/27/15 10:32 AM, Kai Jannusch wrote: Dear all, After my analysis for pial_lgi using fsaverage as common space subject, I started a Monte Carlo correction in Qdec. The terminal lists the significant clusters afte

Re: [Freesurfer] extract values of individual cluster‏

You will have to rerun the analysis using mri_glmfit-sim. This will create a text file with a list of values for each subject. Run mri_glmfit-sim with --help to get more info On 8/26/15 11:55 AM, pablo najt wrote: Dear FS experts, Reposting my message below. Thanks I have run two group compa

Re: [Freesurfer] slice timing correction fmcstc files are lacking

what slice order was the data created with? Find out and then use that slice order in the command On 8/26/15 4:14 AM, std...@virgilio.it wrote: Hi list, I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run. I have acqui

Re: [Freesurfer] fast_selxavg3 ( ) failed\n

x27;d go to the appropriate folder 'Projects' and rerun the same > fast-selxavg3 script. > I'd get the same error message, i.e. matlab: command not found > again any thoughts on this would be greatly appreciated. > Thanks > Chaz > > On Fri, 21 Aug 2015 14:15:05 -040

Re: [Freesurfer] mri_volsynth

some of this is answered if you run the command with --help On 8/31/15 3:33 PM, John Anderson wrote: 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 c

Re: [Freesurfer] converting ROI .label to MNI space for SPM8

I'm not sure what is going wrong, but I would use mri_label2vol directly instead of using the combination of mri_convert and tkregister. Instead of passing it a registration file, use --regheader brainmask.mgz On 8/31/15 5:26 PM, Emma Thompson wrote: Forgive me, but I'm re-posting my query b

Re: [Freesurfer] mri_volsynth

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

nship between --dim and --volres? 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 4:06 PM *From:* "Douglas G

Re: [Freesurfer] Did not find any volume geometry information in the surface

need more info, like command lines for mri_glmfit, mri_glmfit-sim, and freeview On 8/31/15 9:27 PM, Erik Lindberg wrote: Hi, I am running mri_glmfit followed by mri_glmfit-sim running the left hemisphere everything works perfect all the way to the visualization in freeview - then I just chif

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

, 2015, at 2:05 PM, Douglas N Greve wrote: yes On 08/25/2015 01:11 PM, fmri wrote: Should we run this after recon-all autorecon2-noaseg -subjid ? On Aug 25, 2015, at 7:43 AM, Douglas Greve wrote: Run recon-all -aparc2aseg On 8/24/15 7:00 PM, fmri wrote: Hello FreeSurfer, How do I get edits made

Re: [Freesurfer] cluster info

If you binarize the cluster (ie, cluster=1 evertying else = 0), then you can run mri_segstats with aseg.mgz as the seg, --default-ctab, and your binarized cluster as input. The "mean" column will then be the fraction of the cluster in the ROI. Also, if the sig.mgh is 2mm in fsaverage space, the

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

edit aseg.mgz 2. -autorecon2-noaseg -subjid mysubject* 3. recon-all -aparc2aseg 4. mri_aparc2aseg --s subject --volmask On Sep 1, 2015, at 2:45 AM, Douglas Greve wrote: Try running mri_aparc2aseg --s subject --volmask On 8/31/15 10:51 PM, fmri wrote: after several attempts with mul

Re: [Freesurfer] converting ROI .label to MNI space for SPM8

AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I'm not sure what is going wrong, but I would use mri_label2vol directly instead of using the combination of mri_convert and tkregister. Instead of passing it a registration file, use --regheader brainmask.mgz

Re: [Freesurfer] cluster info

ting are adding up to more than one. Is this number the faction of the ROI that the cluster is covering? Tracy *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Dougl

Re: [Freesurfer] mri_pretess on fsaverage

you can also use mri_binarize with the --surf option On 9/5/15 9:32 AM, Bruce Fischl wrote: > Hi Noam > > yes, you should be able to run mri_pretess (or mri_mc) on any volume to > generate a tessellation of any label in the volume you specify > > cheers > Bruce > On Thu, 3 Sep > 2015, Peled, Noam

Re: [Freesurfer] Segmenting deep and outer white matter

The best thing is to take a look at the wmparc. It was not really designed to be deep and superficial. There is only one "deep" WM seg which is called "Unsgemented White Matter" or something like that. doug On 9/5/15 5:54 PM, Bruce Fischl wrote: Hi John I defer to Doug. Not sure he ever publ

Re: [Freesurfer] Register.dof6.dat missing

If you want the one in the bold folder, then you need to run with -per-session. In general you should include a command line when you post a question. doug On 9/10/15 10:21 AM, Rodriguez-Thompson, Anais wrote: > Hi Freesurfer experts, > > One of my subjects is missing the register.dof6.dat file

Re: [Freesurfer] White matter volume

The values in wmparc.stats will have partial volume correction. The onesfrom fslstats will not. On 9/12/15 3:44 PM, John Anderson wrote: Hi Bruce, Kindly I want to inquire about the _difference between_ white matter volume generated by freesurfer ( specifically the white matter parcellation

Re: [Freesurfer] How to create a FSGD file

Create it with a text editor, there is no command. On 9/14/15 9:37 AM, nellie wrote: Dear Freesurfer engineers, According to the introduction of Wiki, I know theexact structure of alegal FSGD file. However, I still don't know how to create a FSGD file, for example, using which command or t

Re: [Freesurfer] Question about the raw thickness range

For #2, that option won't do anything, but it probably needs to be there. On 9/16/15 8:28 AM, Bruce Fischl wrote: Hi Feng I'll answer 1. and leave 2 for someone else (Doug?). We have a hard limit on the max thickness of 5 but no lower bound other than 0 of course. This prevents large values d

Re: [Freesurfer] cortical thickness of a volume-defined ROI

you don't have write permission to that folder. Get write permission or put the reg file in a different place On 9/16/15 9:45 AM, Lim, Lena wrote: Dear Experts, I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm analysis following the instructions (https://surfer.n

Re: [Freesurfer] glmf-fit with 8 categorical variables

That is not going to work because you have way more regressors than you have data points. doug On 9/16/15 9:05 AM, Kallirroi Retzepi wrote: > Hello, > I am trying to run glm-fit on a total of 36 subjects - there are 8 > categorical variables (group, smoking, gender etc) and one continuous > (age)

Re: [Freesurfer] Freesurfer/Qdec brain images

Hi Lena, QDEC does not have that much functionality, so you may have to move to tksurfer or freeview. More answers below. On 9/16/15 10:05 AM, Lim, Lena wrote: Dear Experts, I need some help regarding saving the brain images in Freesurfer/Qdec please: 1) Can I save the brain regions shown

Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer

On 9/21/15 9:15 PM, chenhf_uestc wrote: Hi, Douglas Thanks for your reply. I have two further questions here. First, I know that --grf is gaussian random fields for the volume (not surface). Could the Monte Carlo simulation such as "--cache 4 neg" be used for correction on volume? Because t

Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

Yes, that is fine as long as they are listed as discrete variables (as is the case below). doug On 9/22/15 7:59 AM, pablo najt wrote: Hello Douglas, If I understand your comment about defining all discrete variables as classes (e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command line s

Re: [Freesurfer] Non-matching ROI areal measures using mri_segstats and mris_anatomical_stats (2nd post)

Sorry, I thought I had answered this (or something like it) recently. When transforming area (or volume) with mri_surf2surf you have to turn on jacobian correction with --jac. Try that and see if the results are similar doug On 9/22/15 8:58 AM, julienbesle wrote: > I am reposting this message,

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

If you intend to compute a slope for each subject (first level mri_glmfit), then input the slopes to the 2nd level to test for effects of interest. Is this what you mean? It is probably possible to do this with a single FSGD file and single command line, but it is much easier to set up and und

Re: [Freesurfer] Convert volume to surface

Try using the mri_binarize below with the --surf option. You'll probably want to add a little smoothing with --surf-smooth 2 or so ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 9/27/15 4:58 AM, Martin Tisdall wrote: > Could you talk me through the best way to co

Re: [Freesurfer] dt_recon

On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote: Hi Doug and Bruce, After running the command : dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>> I need to generate the final statistics ( FA for every

Re: [Freesurfer] WMPARC fsaverage

I made one and put it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz Note that this should not be used for anything other than visualization, ie, it has little or no scientific value On 9/24/15 6:25 PM, Mohammed Goryawala wrote: ​ Hello FreeSurfer Experts,

Re: [Freesurfer] 3_group_comparison

Did you include the back slashes in your command? If so, remove them and retry. On 9/25/15 7:11 PM, Dusan Hirjak wrote: Dear Freesurfer experts, I am trying to compare 3 groups (aut, sch, ges) according to thickness, area and LGI at once (omnibus test). I did run the following command: mri

Re: [Freesurfer] PVE correction tool within the V 6 beta

I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions.

Re: [Freesurfer] mri_vol2vol binary mask

Add --interp nearest to use nearest neighbor interpolation instead of trilinear On 9/24/15 1:48 AM, Jinsong Tang wrote: Hello, I am try to convert some binary mask (0,1) to native space. I use this command line: mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask _ra

Re: [Freesurfer] Query about the fsgd file and glm model in freesurfer

The 1st is wrong. The 2nd one is correct. You can also look at this page for more info include setting up contrasts https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V On 9/24/15 3:54 AM, chenhf_uestc wrote: Dear freesurfer experts, I have some questions about the statistical model in frees

Re: [Freesurfer] Question about the volume conversion in freesurfer

This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compu

Re: [Freesurfer] Aparcstats2table Insula Thickness is Zero

Can you send the command and terminal output? On 9/24/15 2:23 PM, Popal, Haroon (NIH/NIMH) [F] wrote: Hello, When I use aparcstats2table to pull thickness values of the Desikan atlas, I get a value of zero for two of my subject’s insula thickness in both hemispheres. For these two subjects, I

Re: [Freesurfer] total grey matter volume

Not for thickness. For surface area it is a good idea to do some kind of normalization. Typically people use the estimated intracranial volume (ICV). You can also use total brain volume or total grey volume. You just need to be aware that each one of these tests something different. On 9/2

Re: [Freesurfer] total grey matter volume

etc. within each group? Thanks again, Lena *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* 28 September 2015 17:18 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] total grey matter volume Not

Re: [Freesurfer] Parcellation stats

what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness a

Re: [Freesurfer] problem fast_selxavg3b

oops, sorry, that did not make it into the distribution. You can get it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m thanks doug On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: > Dear members of the freesurfer mailing list, > > I'm using freesurfer-L

Re: [Freesurfer] Sulc value of given Tal coordinates

when you load the fsaverage surface into freeview or tksurfer you will see some coordinates, those coordinates will be MNI305 coords. If you map the individual sulc or curv into fsaverage space and load is as an overlay, then you can see what the sulc/curv value is at a given coordinate. On 9/2

Re: [Freesurfer] qdec error

Try normalizing the continuous covariates (ie, subtract the mean and divide by the stddev) On 9/29/15 9:16 AM, Lim, Lena wrote: > Thanks, Amanda. Yep, I did that. It works alright if I removed IQ and used > only Age and Gender as covariates... > > > -Original Message- > From: freesurfer

Re: [Freesurfer] warping surface label to volume space

Can you upload the subject so I can look at it? On 9/29/15 9:05 AM, Jacobs H (NP) wrote: Hi Doug, The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong? Best Heidi Van: freesurfer-boun..

Re: [Freesurfer] warping surface label to volume space

filedrop2 url at the end of this email On 9/29/15 10:34 AM, Jacobs H (NP) wrote: Sure, where should I upload it to? Thanks! Heidi From: Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday

Re: [Freesurfer] GRF correction in mri_glmfit-sim

On 9/29/15 11:32 AM, chenhf_uestc wrote: I am also very interested in these questions, but I do not find the response. Could anyone provide the answers? Thanks, Feng *发件人：*"Meiling Li" *发送时间：*2015-09-22 22:09

Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

On 9/29/15 10:59 AM, chenhf_uestc wrote: Dear Freesurfer experts, In the stats folder of subject in the SUBJECTS_DIR, I found the files of lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results belong to two different atlas? *Because the values and brain regions are diff

Re: [Freesurfer] Questions about fsgd file & contrast

1) You don't include sex as a covariate. Include it as a class (ie, Class Male and Class Female rather than Class Main). 2) You need to include Minutes in your null hypothesis. 3) Include minutes as a covariate as you have done, then create the proper contrast matrix. The contrast matrix will de

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

please send the terminal output that includes the error On 6/1/16 8:10 AM, Hao wen wrote: Hello, freesurfers: I am doing group analysis, with two diff groups, so I want to know that how to create my own Contrast and Design matrix, because that I know in QDEC and CMline, in the freesurfer wik

Re: [Freesurfer] mris_preproc - srcsubjreg

I would not expect the glm to change much, but the activation might shift around a little depending upon your new target. On 6/1/16 11:18 AM, Makaretz, Sara Johanna wrote: > Thank you! Does this mean that an older glm would have still used fsaverage > for the "common surf" but then the output is

Re: [Freesurfer] FC from resting-state

You should first check your func-anat registration with tkregister-sess On 6/1/16 11:20 AM, Martin Juneja wrote: Hello FreeSurfer experts, I am working on resting-state functional connectivity using freesurfer by following the instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFast

Re: [Freesurfer] Input for mris_fwhm to generate fwhm.dat file

It is the error in the model fit. If you run mri_glmfit with --save-eres it will save a file called eres.mgh. this is the residual file On 6/3/16 6:29 PM, Chung, Yoonho wrote: Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@

Re: [Freesurfer] SAVE REG in tkregister2

That will work in version 6 On 6/7/16 4:55 AM, Hao wen wrote: Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized. I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Manual

Re: [Freesurfer] SAVE REG in tkregister2

what is your command line? On 6/7/16 4:46 AM, Hao wen wrote: Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL I think maybe this is a very stupid question:)

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

gt; > Hi, thanks for your reply, here is the output of the terminal in txt > > file, hope to hear from you soon > > Merci > > Hao > > > > *De :* freesurfer-boun...@nmr.mgh.harvard.edu > > de la part de Douglas Greve > > > > *Envoyé :* me

Re: [Freesurfer] cespct in FS 5.3

Rescaling by the voxel mean will mess up the intensity normalization. Try making your analysis (mkanalysis-sess) with -no-inorm and see if the results are more consistent. They will not be exact because the raw mean time course is not used to create the cespct. Rather it is the regression coe

Re: [Freesurfer] Coordinate system in mris_convert

Try adding --cras_correction to the command line and see if it works. On 6/7/16 10:27 AM, Alexandre Routier wrote: Hello, I would like to work with mesh representation of pial and white surfaces in vtk format. To do that, I use the following syntax: mris_convert lh.pial lh.pial.vtk However,

Re: [Freesurfer] SAVE REG in tkregister2

sion 6? thanks *De :* freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve *Envoyé :* mardi 7 juin 2016 15:54:46 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] SAVE REG in tkregister2 That will w

Re: [Freesurfer] Coordinate system in mris_convert

if it helps. By the way, I was wondering: why this c_ras vector is not taken into by default e.g. with mris_convert or mri_tesselate ? 2016-06-07 16:54 GMT+02:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>: Try adding --cras_correction to the command line and see if it work

Re: [Freesurfer] Coordinate system in mris_convert

Try the group analysis tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 6/8/16 2:39 AM, Dave Yas wrote: Hello all, I'm new to surface analysis. I have 2 groups (patient and healthy control) that i want to check differences between. I want to perform cortical thi

Re: [Freesurfer] selxavg3-sess error

Do you have both polar and eccen data? If so, can you send the Xtmp.mat file? On 6/8/16 6:08 AM, Francesca Strappini wrote: Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinoto

Re: [Freesurfer] aseg.stats and aparc.stats reliability

Johnathan, can you point us to source of the issues you are concerned about? Is there a paper or website? thanks doug On 6/8/16 9:46 AM, Bruce Fischl wrote: > Hi Jonathan > > as far as we know, FreeSurfer is the most reliable and robust > longitudinal brain morphometry tool that is publicly avai

Re: [Freesurfer] contrast

I responded in the body of the email On 6/9/16 7:57 PM, Dave Yas wrote: /*Helllo! That was an empty email! */ > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Thu, 9 Jun 2016 16:33:48 -0400 > Subject: Re: [Freesurfer] contrast > > > > On 06/08/2016 11:40 PM, Dave

Re: [Freesurfer] Remove zeroes from mri_segstats in mean calculation?

You can include a mask, eg mri_segstats --i input.nii.gz --mask input.nii.gz --maskthresh .0001 On 6/10/16 11:59 AM, Lakhani, Bimal wrote: Hello, I am running mri_segstats to get the intensity mean of a custom image volume, but I do not want zeroes to be included in the calculation of t

Re: [Freesurfer] Define the design matrix by myself

sorry, I don't understand the question. It looks like the design matrix is right. It looks like the contrasts tests for a diff between AD and controls. What else do you need? On 6/13/16 8:49 AM, Hao wen wrote: Hello: I am still confused about how to make the design matrix in FS for group an

Re: [Freesurfer] swapped dimensions?

What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder On 6/13/16 9:57 PM, Marja Caverlé wrote: Hi Bruce, I converted first of all because freesurfer d

Re: [Freesurfer] Define the design matrix by myself

, I dont want the interact between group and gender Hope to hear from you soon! Merci Hao *De :* freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve *Envoyé :* mardi 14 juin 2016 04:20:18 *À :* freesurfer

Re: [Freesurfer] Define the design matrix by myself

interact between group and gender Hope to hear from you soon! Merci Hao *De :* freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve *Envoyé :* mardi 14 juin 2016 04:20:18 *À :* freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] output file from running mri_glmfit-sim

On 6/8/16 9:51 AM, Yu Sun Chung wrote: Hi, all, While working on gyrification data using Freesurfer, I have a question to confirm one of output files. First, I did run mri_glmfit using age x IQ itneraction. fsgd file in which I included intracranial volume and gender to covary out. then, I

Re: [Freesurfer] SAVE REG in tkregister2

manual ... Thank you and the bbregister, the flag will work in version 6? thanks *De :* freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve *Envoyé :* mardi 7 juin 2016 15:54:46 *À :* Freesurfer suppor

Re: [Freesurfer] Define the design matrix by myself

on Merci! *De :* freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve *Envoyé :* mardi 14 juin 2016 17:23:08 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself When passed to mris_preproc

Re: [Freesurfer] Coregister the CT image and MRI image

use mri_vol2vol, like mri_vol2vol --mov CT.nii --reg v1t2.lta --fstarg --o CT-in-anat.nii On 6/15/16 9:58 AM, HARI GURAGAIN wrote: Dear Douglas, With the suggestions from Zeke, the mri_coreg is working now. I have one last question: I got the new v1to2.lta. How to apply this transformation to

Re: [Freesurfer] Convert ascii to .mgh

I would do it in matlab, eg, F = MRIread('F.mgh'); % This is to get the proper header information lfdr = load('lfdr.asc'); F.vol = fast_mat2vol(lfdr,F.volsize); MRIwrite(F,'lfdr.mgh'); On 6/15/16 4:45 AM, Robby De Pauw wrote: Dear FreeSurfer users, To address the problem of multiple compar

Re: [Freesurfer] convert from MNI152 to native space

You'll need a registration that goes from the functional to the mni152. This has to be done in two steps, 1. Run mni152reg --s subject to create the anat-to-mni152 registration (needs FSL) 2. Run bbregister to get the anat-to-func reg (in lta format) 3. then combine them with mri_concatenate_

Re: [Freesurfer] Found 0 unique series

You don't need a .dat file, it just could not create the file. It was trying to create it in /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/ do you have write permissions into that folder? On 6/15/16 5:01 PM, Raney, Talia L. wrote: > This is true, but in other subje

Re: [Freesurfer] GLM_Fit Question

try now On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order

Re: [Freesurfer] Error loading a constructed annotation file

It does look like the problem is the rh.orig. Do you have read permissions for that file? It may be that the file is corrupt. Can you load just that file in freeview or tksurfer? If not, you can try to regenerate it by running mris_fix_topology (look in the subject/scripts/recon-all.log file fo

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

fer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today'

Re: [Freesurfer] FSFAST- Cerebellum

After you run preproc-sess, there will be a file called register.dof6.dat. Map fmri into the anatomical space, something like mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz However, I don't

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

You have no HDFemales so the 2nd column is 0. On 6/21/16 7:40 PM, Arkadiy Maksimovskiy wrote: Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y lh.BD_SD.thickness.

Re: [Freesurfer] Converting fsaverage to MNI space

Try mri_vol2vol --targ fsaverage.DKT40+aseg.nii --mov /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --o fsaverage_MNI_DKT40+aseg.nii --interp nearest --reg /Applications/freesurfer/average/mni152.register.dat --inv On 6/22/16 12:45 AM, Skyler Gabriel Shollenbarger wrote: Hi FS communi

Re: [Freesurfer] doubts

Does that file exist? What is in it? If it is empty, it may bneed to be regenerated for that subject. Run recon-all -s subject -segstats On 6/22/16 7:17 PM, Elias Vergílio Da Cás wrote: Hi, *After the command: * asegstats2table --subjects AntonioMagnani -- meas volume --tablefile TESTE.tx

Re: [Freesurfer] FSFAST- Cerebellum

yes On 6/24/16 9:19 AM, Thomas Yeo wrote: > Hi Doug, > > Would your mri_segstats command work if instead of aseg.mgz, Sabin > passed in the cerbellum parcellation in the same anatomical space as > aseg? > > --Thomas > > On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve

Re: [Freesurfer] Order of overlays

Yes, you can. If I remember correctly, you can goto view->configure overlay, then find the item to specify that you want the labels under the activation. On 6/29/16 5:22 AM, Reza Rajimehr wrote: Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The

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