Re: [Freesurfer] mri_surfcluster

use this program ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr On 7/6/16 9:22 AM, tom parker wrote: Dear Freesurfers, I ran a comparison between different groups using mri_glmfit. Now I would like to correct the results in sig.mgh by multiple comparisons using FDR.

Re: [Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

See if this page helps http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats On 7/6/16 9:07 AM, Kaiming Yin wrote: Dear experts, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and

Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

what do you mean nothing happens? After you hit the return key, it should either give you the path to the command or it should say Command not found. doug ps. Please remember to post to the list and not to us individually On 7/8/16 7:16 PM, Erik Jahner wrote: When I type "which matlab” in t

Re: [Freesurfer] mri_segstats

Register the suvr to the anatomical (mri_coreg) then use mri_vol2vol On 7/18/16 6:58 PM, Alshikho, Mohamad J. wrote: > Thank you Doug, > Kindly how can I make the suvr and the anatomical images in the same slice? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [ma

Re: [Freesurfer] PVE correction tool on Freesurfer 6

the response is in the body f the mail On 7/18/16 9:27 PM, Lee Subin Kristine wrote: Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as always, Subin ---

Re: [Freesurfer] registering subject pial to fsaverage

I don't understand what you did or what the problem is. Can you elaborate? On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote: Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on? On 7/19/16 1:57 PM, Koubiyr, Ismail wrote: I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header. Here is the version of FS I

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

, which is weird because it was not working before … Any idea what might be the problem on my system ? Thanks again. Ismail On Jul 19, 2016, at 10:32 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I used the same version, but I used it on linux. Do you have a linux box w

Re: [Freesurfer] ERROR: cannot find volume matching

What is the exact name of the file that you are trying to include as a taskreg? On 7/25/16 12:26 AM, Erik Jahner wrote: Dear Free Surfer experts I am attempting to run a functional connectivity analysis on some resting state data. However, I keep getting stuck in this final step of the onli

Re: [Freesurfer] How to apply ACPC alignment to Freesurfer output

If you have a registration matrix that maps to the desired orientation, then you can apply it to a segmentation with mri_label2vol. But why not just register the anatomical to the DTI (bbregister) and then run mri_label2vol with that registration to map the WM mask directly into the native DTI

Re: [Freesurfer] mri_label2label volume registration problem

When you use --regmethod volume, it assumes that the label coordinates are in native anatomical space and then applies the mni305 registration (talairach.xfm). In this case, your source subject is fsaverage so the native space is assumed to be mni305 space (and talairach.xfm is the identity). S

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

Can you send your new fsgd file and new design matrix? On 7/24/16 6:06 PM, miracle ozzoude wrote: Hello Doug or Bruce, I demeaned and normalize like you suggested but I'm still getting the same results. I created a new fsgd file using the demeaned and normalized variables (n = (x-mean)/std(x)

Re: [Freesurfer] bbregister problem in FS5.1

It looks like one of two things: 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, AFNI) can read the file 2. You have run out of disk space On 7/24/16 10:52 AM, Fred Sampedro wrote: Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 an

Re: [Freesurfer] normalizing in fsgd

No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand. On 7/24/16 1:33 PM, miracle ozzoude wrote: Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_g

Re: [Freesurfer] normalizing in fsgd

Actually, I checked the code and found that I had already put a flag in there to do this (I'm so clever). Add ReScaleFlag 1 in addition to DeMeanFlag 1 On 7/25/16 11:22 AM, Douglas Greve wrote: No, that flag does not exist, but it is a good idea! You'll have to normalize th

Re: [Freesurfer] bbregister problem in FS5.1

oblem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine. :( On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: It looks like one of two things: 1

Re: [Freesurfer] Running Several Versions of fsfast GLM In Parallel Leads to "Stale File Handles"

Try this: on line 160 of preproc-sess, change if(-w .) then to if(-w . && $nolog != 1) I think that should do it. On 7/25/16 7:53 PM, Taylor, Johnmark wrote: Hello, I have been trying to run several versions of the same GLM analysis, trying out different parameters to see if they aff

Re: [Freesurfer] Freesurfer 6.0?

We are working pretty hard to get it out but we are still reluctant to set a hard date. I think we'll have a beta version in two weeks, but that's just a guess. doug On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote: Hi there Do we have a potential date for the Freesurfer 6.0 release? I was

Re: [Freesurfer] GLM significance table

The -log10(p) is signed by the sign of the contrast, so to get back to the p value you must compute 10^-abs(sig). On 7/26/16 10:42 AM, Caroline Beelen wrote: Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g

Re: [Freesurfer] How does Optseq2 arrange order of conditions?

On 7/29/16 3:17 AM, 連 志浩 wrote: Hello all, I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got some sequences and read Dale (1999). I'll be grateful to anyone can provide help. 1. I'm curious about why optseq2 arranged the order of conditions, does anyone can

Re: [Freesurfer] brain mask and T1 are not the same size

So you're saying that the dimension changed after you ran freeview and saved the volume? Can you replicate it? ie, if you make a copy of the brainmask.mgz, then edit the copy, does it do the same thing every time you make a copy and edit it? On 7/29/16 12:09 PM, Isabelle Deschamps wrote: Dea

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

Try setting thmin to something small but non-zero (eg, 10e-6) On 8/1/16 10:23 AM, Sabin Khadka wrote: Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka mailto:mr.sabinkha...@gmail.com>> wrote: Hi Doug, I tried to pick up from the thread below to get MNI coo

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

ps. you can always just load the xyz in the label into matlab and compute the centroid On 8/1/16 10:23 AM, Sabin Khadka wrote: Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka mailto:mr.sabinkha...@gmail.com>> wrote: Hi Doug, I tried to pick up from the threa

Re: [Freesurfer] Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)

The contrasts are correct. I think you have done the right thing (or as good as you can) in controlling for the scanners. On 8/1/16 10:46 AM, Oana Georgiana Rus wrote: Dear FreeSurfer Experts, I want to compare structural measures(eg. thickness) between patients and controls controling fo

Re: [Freesurfer] ALE map to surface

You need to run recon-all on the MNI152 T1 brain, then run mri_vol2surf passing your activation map to --mov and with --regheader, then run freeview to visualize On 8/1/16 6:38 PM, Carla Ammons wrote: Hi! I am new to freesurfer so this may be a basic question. I have an activation map (.ni

Re: [Freesurfer] Fwd: question about volume of mask

Hi Dorsa, please remember to include previous correspondence. I'm not sure what you are referring to, but when you reslice a volume, the size of the voxels usually changes so it is impossible to have exactly the same volume. Probably the original file is closest On 7/29/16 12:08 PM, Dorsa Haj

Re: [Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors

Unfortunately, the way I have the retinotopy analysis set up, both polar and eccen must be there. However, you can just copy the polar into a new folder and call it eccen and it should complete. Then you can ignore the eccen part. On 7/29/16 3:04 PM, Taylor, Johnmark wrote: Hello, I am tryi

Re: [Freesurfer] Where are time series from adjusted (post selxavg3) ROIs

Run selxavg3-sess with -svres. This will create a new folder called "eres" in the output analysis directory where the residuals will be stored. Assuming that you have mapped your data to fsaverage space, you can then create a post cing label (mri_annotation2label) and then use mri_segstats wit

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

I think there is an example on the wiki in the ROI analysis section. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs

Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

That recon-all command will not work as the FLAIR input should be a simple FLAIR image. The FLAIR will only correct the pial surface and will have nothing to do with lesion segmentation. Emily Lindermer has a tool that can take a T1 and FLAIR and produce a lesion map; but given that you already

Re: [Freesurfer] Labels to MNI152, SPM compatible

From the names, it looks like both the seg vol and the template vol are both in mni152. Where did Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come from? One thing you can try is to invert the registration by adding --invertmtx to the command line. On 8/2/16 8:18 AM, M

Re: [Freesurfer] mapping error

what is your command line? On 8/3/16 6:00 AM, Caroline Beelen wrote: Dear FS, An aparc.annot ctab file was created but I got the following error: Colortable:aparc.annot.ctab Annotname: myaparc Nhitsfile nhits.mgh Nlabels 6 Labeltresh 0 0.0 Loading freesurfer/fsaverage/surf/lh.orig

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

On 8/3/16 3:45 AM, Ajay Kurani wrote: Hi Doug, Thank you very much for your update regarding this issue. 1)Just curious, will LGI be included in this report as this is another analysis of interest? I was not planning to. The 809 subjects that I used for thickness do not have lGI run on th

Re: [Freesurfer] mri_label2label holes

Hi Fred, I think there are problems with trying to use v6 binaries without the v6 distribution. Zeke may have more of an idea. doug On 8/4/16 4:32 AM, Fred Dick wrote: Dear Doug et al I was doing some cross-subject label morphing over a bunch of subjects (a big continuous patch of vertices)

Re: [Freesurfer] mri_label2label holes

Note that this is a development version and should not be used to run recon-all On 8/4/16 9:02 AM, zkauf...@nmr.mgh.harvard.edu wrote: > Hello Fred, > > Yes, newer development binaries on Mac are not compatible with previous > releases of freesurfer. If you wish the use a newer binary you will n

Re: [Freesurfer] FSFAST ROI atlas

I have not used them myself. On 8/15/16 10:23 AM, Sabin Khadka wrote: HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois

Re: [Freesurfer] Zero cortical thickness

what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location? On 8/15/16 4:13 PM, A Nunes wrote: > Hi, > > I have read in the mailing list about zero cortical thickness, but I > still have some doubts. > > I am calculating the average cortical thickness of s

Re: [Freesurfer] recon-all version update not showing in log file

It will not overwrite the log file so as to retain everything that has been done to the data set; new information is appended to the end of it. On 8/17/16 3:58 AM, Donna Cosgrove wrote: Hi, I am updating previously recon'd datasets done with FS versions 4.4 and 5.2 to v5.3. I'm running the r

Re: [Freesurfer] error in manual edit by freeview

I'm not sure what you are describing. Can you send a picture? On 8/17/16 8:42 AM, 陈聪 wrote: > Hi dear all > I am using freeview to edit segmentation, I found one slice in coronal > view in brainmask.mgz mismatch with other slice, this slice obviously move > down. WM and T1.mgz are normal,

Re: [Freesurfer] Recon-all Correcting Defect 0

Can you send the log file? On 8/17/16 8:46 AM, Heidi Foo wrote: Dear FreeSurfer team, I am currently running recon-all for my subjects but for 2 of them, it stops at correcting defect. Do you have any ideas how I can deal with this problem? Thanks. Regards, Heidi Foo ___

Re: [Freesurfer] FSFAST ROI atlas

d out how aparc+aseg.mgz is created On 8/17/16 9:28 AM, Sabin Khadka wrote: Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done. Thanks for your help! Cheers, Sabin Khadka On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve mail

Re: [Freesurfer] Mixed anisotropic data

It will have some effect, but it is not clear exactly what. Probably the difference in 1.5 and 3T will be bigger. See the paper by Jorge Jovicich for more info about the diffs between 1.5 and 3T. You should make sure to have a balanced design if you want to publish it. On 8/16/16 4:52 PM, Mah

Re: [Freesurfer] FA/MD.nii to fsaverage space

First register the DTI to the anatomical with bbregister to create a register.dat file for each DTI (you can use the same one for FA and MD; for the "mov" volume, use whatever reference you used for motion correction). You can then run mri_vol2surf --mov FA.nii --reg register.dat --projfrac 0.

Re: [Freesurfer] label analysis

Use mris_anatomical_stats On 8/18/16 9:53 AM, Raffaele Dubbioso wrote: Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I r

Re: [Freesurfer] voxel values in destrieux file

Sorry, that is a bug. I introduced it in a change a few months ago. I'll fix it. Thanks! On 8/19/16 11:08 AM, pierre deman wrote: Hello, I am looking at the destrieux atlas generated by recon-all (I use the freesurfer dev version), the file aparc.a2009+aseg.mgz), and sometimes the value of

Re: [Freesurfer] voxel values in destrieux file

The error is in recon-all. If you want to fix this one outside of recon-all you can run cd $SUBJECTS_DIR/subject/mri mri_aparc2aseg --s subject --volmask --aseg aseg.presurf.hypos --a2009s On 8/19/16 11:08 AM, pierre deman wrote: Hello, I am looking at the destrieux atlas generated by recon-a

Re: [Freesurfer] Question re extracting average thickness values per subject based on cache.th13.abs.y.ocn.dat

On 8/19/16 5:21 PM, Gold, Andrea (NIH/NIMH) [F] wrote: Hi, I’m trying to extract the average thickness per subject in significant clusters from a Qdec analysis, and hope to clarify 2 things re: the “cache.th13.abs.y.ocn.dat“ output from this command: mri_glmfit-sim --glmdir (dir) --cache 1

[Freesurfer] version 6 NOT released yet

PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT. Thanks The FreeSurfer Team ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] Fs 6.0 dev version update

Hi Renata, version 6 is not ready and should not be used. As far as we know, there is not a link to 6.0 anywhere on our web pages. Where did you find it? doug On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote: Dear FS experts, I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and no

Re: [Freesurfer] version 6 NOT released yet

I don't know. This is a question for Eugenio On 8/24/16 11:53 AM, pedrogomesr...@gmail.com wrote: Hi, Doug. Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 recons, or this also should not be done? Best, Pedro Rosa. On Aug 24, 2016, at 11:58, Douglas

Re: [Freesurfer] Fwd: Cannot allocate memory mri_glmfit to remove covariates

This looks like it is a binary matlab file. This should be a simple text ascii file. On 8/24/16 9:01 PM, Heidi Foo wrote: Hi Douglas, Attached the covariates.mat file. Thanks. Regards, Heidi Foo -- Forwarded message -- From: *Douglas N Greve*

Re: [Freesurfer] Questions about surface coordanates

tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you should see something like the following print out selected vertex 123491 out of 163842 current -39.11 15.65 11.26 orig -55.67 -10.37

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

By "wrong" I meant that permutation no longer gives exact p-values in expectation with non-orthogonal designs. There is no theory to characterize the accuracy of Freeman-Lane of the other methods. In this sense, they are not approximations but ad hoc methods that people hope do a better job t

Re: [Freesurfer] rfMRI and T2w image

You don't need T2w to run FreeSurfer/recon-all. There is an option to add a T2, but it is not necessary. In any event, you will not be able to use an fMRI scan for this purpose. On 8/30/16 7:50 AM, Dev vasu wrote: Dear Sir, In order to run my structural analysis pipeline , i require T2w im

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out On 8/30/16 10:12 AM, Krieger, Donald N. wrote: Dear list: What are the advantages of including a T2 scan when running recon-all –all ? Which results can it effect and to what extent? And how sensitive is freesurfer

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Hi Don, the T2 stream is a work-in-progress, so we don't have a lot of these answers. In theory, a T2 will allow better placement of the pial surface allowing it to better exclude dura. No publication on this yet. doug On 8/30/16 10:12 AM, Krieger, Donald N. wrote: Dear list: What are t

Re: [Freesurfer] Questions about surface coordanates

confusing. Thanks! Kindly, Islem On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you

Re: [Freesurfer] REPOST: problem with Qdecrc file

Try long_mris_slopes On 8/31/16 8:34 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I still don't seem to be able to choose spc and rate etc from the dropdown > menu in QDEC. Is there an option to perform the longitudinal 2 stage model in > the command line instead of QDEC? > > Thank you!

Re: [Freesurfer] 答复: Questions about surface coordanates

...@nmr.mgh.harvard.edu] *代表 *Douglas Greve *发送时间:*2016年8月30日21:21 *收件人:*freesurfer@nmr.mgh.harvard.edu *主题:*Re: [Freesurfer] Questions about surface coordanates tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Is your matrix a simple ascii text file? If so, please send. On 9/9/16 11:00 AM, Smaragdi A. wrote: > Dear mailinglist, > > I get the following error when I run the mri_glmfit: > > MatrixReadTxT: could not scan value [8][360] > WARNING: matlab elment type is 805908489, which is not a ma

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

__ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: 09 September 2016 16:20 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360] Is your matrix a si

Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis

Did you verify that the result of mni152reg is accurate? It should have printed out a command line to check it On 9/9/16 5:58 AM, Matyáš Kuhn wrote: > Hi FreeSurfer experts, > > We would like to use Destrieux atlas for masking DLPFC in subjects, who > uderwent fMRI and we used SPM to process the

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1

You can try normalizing your covariates. You can do so before putting them into the fsgd file or you can add the following two lines to your fsgd file: DeMeanFlag 1 ReScaleFlag 1 On 9/9/16 11:25 PM, Seung Gul Kang wrote: Hi, I am new learner in freesurfer and analyzing the difference of t

Re: [Freesurfer] Tkregister2 error, moveable not present just white screen

What is your command line and log file? Sounds like the initial registration failed. On 9/11/16 10:04 PM, A Nunes wrote: Hi, After doing a bbregistration I visualized the results with tkregister2. The target is alright, however, the moveable is not present, it is just a white screen. What

Re: [Freesurfer] convert FSFAST files to gifti format

not sure, maybe one of the HCP folks could weigh in. You might try converting the lh.nii.gz to mgh file first. Should not make a difference, but it might On 9/14/16 10:24 AM, Sabin Khadka wrote: Doug- I did try mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white $SUBJECTS_DIR/sub/REST/bold/001

Re: [Freesurfer] Coordinates of particular volumes (fwd)

the command should be [i,j,k] = ind2sub(mri.volsize,pos); -- Forwarded message -- Date: Tue, 27 Sep 2016 13:00:51 +0700 From: Aziz Nanthaamornphong Reply-To: Freesurfer support list To: Freesurfer support list Subject: Re: [Freesurfer] Coordinates of particular volumes I have

Re: [Freesurfer] Co-registering different source data

Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd. On 9/27/16 9:38 AM, Crawford, Anna wrote: > Hi, > > I keep getting an error when I use mri_label2label. Below is my input and > output. I have tried various paths all the

Re: [Freesurfer] Question about mri_glmfit

Try normalizing your covariates (ie, subtract the mean and divide by the stddev). On 9/28/16 3:07 PM, kinson li wrote: Hi there, Anyone can help me out? Thank you. 2016-09-28 13:46 GMT-04:00 kinson li >: /Hello,/ /I would like to conduct an analysis us

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

You need to specify --trgsubject ico in mri_vol2surf On 9/28/16 3:01 PM, Jared Zimmerman wrote: > Hi All, forwarding this message along again as I'm still having some trouble > getting this to work. Basically I would like to 1) project processed > residual time-series from the subject-space vo

Re: [Freesurfer] get non-cortex vertices

It is changing with each subject because each subject's brain is different, and you can't get a subject-specific mask from fsaverage5. Can you load all your data into matlab and then compute a mask based on non-zero voxels? On 9/28/16 1:57 PM, Dorothy Sincasto wrote: Hi freesurfers, I am do

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

Those are not residuals. If you want residuals, you will need to run mri_glmfit from the command line adding --eres-save. You can get the command line from the mri_glmfit.log file in the glmdir On 9/28/16 10:58 AM, Damien MARIE wrote: Dear FreeSurfers, Sorry for the repost. I’m still trying

Re: [Freesurfer] Anatomy File Orientation Question

You do not need to specify that. In fact, you should not because it may mess up the orientation. You do not need to add any special arguments to mri_convert. You can also specify .nii instead of .nii.gz On 9/27/16 3:14 PM, Sepeta, Leigh wrote: Hi all, Sorry to re-post: I am trying to bri

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert

I don't understand what the problem is. Can you elaborate? On 9/27/16 12:13 PM, Tamara Tavares wrote: The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and

Re: [Freesurfer] monte carlo continue/ desktop restarted

There is no way. Yes, you can specify fsaverage for yoursubject On 9/28/16 3:47 PM, miracle ozzoude wrote: Hello Doug, Do you know if there's any command to make it continue from where it stopped in case of future incidents? Also, what does " yoursubject" mean in this code? Can I substitute i

Re: [Freesurfer] Question about mri_glmfit

oblem about covariates. Thank you. Jin 2016-09-28 15:29 GMT-04:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>: Try normalizing your covariates (ie, subtract the mean and divide by the stddev). On 9/28/16 3:07 PM, kinson li wrote: Hi there, Anyone can help

Re: [Freesurfer] optseq help

The command line looks ok. The low efficiency is coming from the low number of events per event type. On 9/27/16 9:52 AM, Alexandre Obert wrote: Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable du

Re: [Freesurfer] Co-registering different source data

t;>> Sent: Tuesday, September 27, 2016 11:36 AM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Anna, if you are using bash the command is: >>>> >>>> export SUBJECTS_DIR= >&

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

urf: Forward Loop (40962) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (112745) Reverse Loop had 72236 hits On Sep 28, 2016, at 3:34 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote: You need to specify --trgsubject ico in mri_vol2surf On 9/28/16 3:

Re: [Freesurfer] mgz file format

No, no PHI gets transferred into the mgz file. On 9/29/16 1:08 AM, prasser wrote: Hi, When using mri_convert to create 001.mgz from dicom that have *not* been anonymized does any patient, institution, study description etc information get transferred into the 001.mgz? Thanks. _

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to me on our filedrop? On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote: Hi Douglas, Please find below the mri_coreg terminal output : / / /$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $/ /cwd /NAS/tupac/matthieu/FS5.

Re: [Freesurfer] mri_average vs mri_concat

What are the pixel values in the mgz file? They should be binary, ie, 1=in a label, 0 = out of label On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote: Overlays in .mgz format using mri_vol2surf -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Oct 5,

Re: [Freesurfer] Extracting thickness values using labels

The easiest way to to re-run mris_preproc without the --paired-diff to get a stack of all your data, then run mri_segstats --i stackwithalldata.smoothed.mgh --seg ocn.mgh --excludeid 0 --avgwf ocn.dat ocn.mgh is the ocn file (output cluster number), and ocn.dat will be a table with each inpu

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

it : Hi Douglas, I have just sent it to you on Filedrop. Best regards, Matthieu 2016-10-03 17:45 GMT+02:00 Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>: Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to me on our filed

Re: [Freesurfer] How to use -openmp flag/ Please help

Also, don't use -qcache until after you have run and manually inspected your analysis On 10/13/16 3:29 PM, Z K wrote: > You provided us with very little information to help you solve your > problem. Please read the "How to describe you problem" section of our wiki: > > https://surfer.nmr.mgh

Re: [Freesurfer] issue with unpacksdcmdir

Could be. Can you run dcmunpack instead of unpacksdcmdir? You should be able to use the same command line. Let me know how it goes. doug On 10/13/16 5:25 PM, Marco Loggia wrote: Hello Doug and Freesurfers, We are having trouble unpacking DTI data collected in Bay7. Data are here: cd /autofs

Re: [Freesurfer] Cortical Thickness Zero Values

The entire medial wall has thickness values of 0 because there is no cortex there. There needs to be a surface in that area because we need a closed surface. On 10/12/16 8:10 PM, Taha Abdullah wrote: Hello All, Quick question, I ran recon-all with the qcache option and after converting the

Re: [Freesurfer] GLM in groups with unequal size

It will be constrained by the group with the smaller number of subjects. There is not anything wrong with unequal group sizes, but it is less efficient than if you had split your acquisitions evenly. On 10/13/16 10:17 AM, Bruce Fischl wrote: Hi Eelco it depends on how you setup your GLM. A

Re: [Freesurfer] GLM in groups with unequal size

It will not On 10/13/16 10:34 AM, Eelco van Duinkerken wrote: Ah sorry for the low level of info. I am aiming to do a simple group comparison, where I'm comparing thickness between controls and obese or T2DM patients, regressing out the effect of age, sex and, hypertension. So I created one t

Re: [Freesurfer] Warping an ROI from one subject to another

So the result of step 4 looks ok on the volume but not on the surface? How are you putting the volume-based ROI back on the surface? This is tricky because now it will be a 1mm thin label. You should use mri_vol2surf for this, maybe selecting the --projfrac-max to make sure that it grabs the v

Re: [Freesurfer] Quantifying volumes

please send command lines On 10/14/16 6:36 AM, Damien MARIE wrote: Hi, Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using

Re: [Freesurfer] No cluster remains significant after multiple comparisons

It may be the case that the result are not significant. If you have an apriori region then you can analyze only in that region rather than doing a whole-brain analysis. That will make the result more significant. On 10/9/16 4:08 PM, Karamfil Bahchevanov wrote: Hello Freesurfer experts, I'm

Re: [Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

You can add --mul 1000 to multiply everything by 1000 On 10/11/16 4:47 PM, Chung, Yoonho wrote: Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following dec

Re: [Freesurfer] group analysis

Both contrasts are right. You might want to change the value from 0.5 to 1/6, but that won't affect the actual p-values (only the gamma values). The 2nd contrast is correct, but it maybe difficult to interpret if the first contrast has an effect. Technically, you should verify that there is n

Re: [Freesurfer] Quantifying volumes

ur help! ​Best regards, Josue *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Friday, October 14, 2016 5:54 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Quantifying volumes please send

Re: [Freesurfer] GLM on cortical and subcortical volume

do you mean volumes of ROIs? Yes, there is a tutorial on this in our wiki, but basically you need to run aparcstats2table and/or asegstats2table to create a table of volumes for each subject and ROI. Then use mrI_glmfit with the --table option instead of --y On 10/18/16 10:18 AM, miracle ozzo

Re: [Freesurfer] GLM on cortical and subcortical volume

the response. Please can you send me the link. Also, does GLM correct for total intracranial volume or do I need to create fsgd file with total intracranial volume as covariate? Thanks On Tue, Oct 18, 2016 at 10:48 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: do yo

Re: [Freesurfer] Cortical Thickness Zero Values

two subjects, is this due to anatomical variability between individuals? I was surprised by the 9,000 values that was missing. On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: The entir

Re: [Freesurfer] mapping ROI to surface space

not necessary. mri_vol2surf by default uses nearest neighbor interpolation On 10/28/16 11:17 AM, Andrews, Derek wrote: > The ROI volume is not binary however I binarized it after mapping to the > surface space. Should I have binarized the ROI prior to running > mri_vol2surf? > > Best, Derek > > >

Re: [Freesurfer] Creating overlay files automatically

We usually create nifti or mgz files to use as overlays both for the volume or the surface. Is this what you mean? On 10/28/16 9:17 AM, Eloy Geenjaar wrote: Dear Freesurfer Experts, I am a student at the technical university of Delft and currently working on a project to automatically visu

Re: [Freesurfer] mris_left_right_register not found

try here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_left_right_register On 10/26/16 1:33 PM, Daya P wrote: Hi All, I was looking to flip a label I created on the left hemisphere to the right hemisphere and I read in previous messages that mris_left_right_register and then mri_app

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