Re: [Freesurfer] multiple comparisons correction

Dear professor, Thanks for your reply. You said that when drawing conclusions from both hemispheres then I need to use .025, but I found that in qdec interface, the default value of -cwpvalue is 0.05. So are they inconsistent? I also want to find a solution about an ERROR. I tried to run a

Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

Hi Michael, yes, you can do this in tksurfer with a tcl script (labl_erode and labl_dilate I believe). Not sure if there is a binary to do it, but it would be pretty easy to write Bruce On Mon, 16 Jul 2012, Michael Waskom wrote: Hmm, ok.  Are there no functions for doing a dilation/erosion

Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

Hmm, ok. Are there no functions for doing a dilation/erosion on a surface label? On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve wrote: > There is not an easy/good way to handle this situation. The way it works > is that it goes through each point in the source and finds the closest > vertex in

[Freesurfer] recon-all for non-human primates failed and what to do next?

Hi, FreeSurfer experts. I have successfully used FreeSurfer to reconstruct monkey brains, but when I used the same scripts on chimpanzees, it failed miserably (see the attached figure). I tried several strategies, such as normalizing the wm.mgz to 110, but the scripts still did not work. Could

Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

Yeah I didn't think so..well my fault for trying to push 30 brains through at a time on just 24 cores and 24 Gigs of RAM, and all started within 10 minutes of each other..froze her up and locked others out. Ahh, well. Thanks Bruce and crew! - Josh On Mon, Jul 16, 2012 at 1:58 PM, Bruce Fischl wro

Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

not that I have any real hope lol - Josh On Mon, Jul 16, 2012 at 1:41 PM, Joshua Lee wrote: > Is it possible/pracitcal? This is a long step, and unfortunately my > analysis computer was rebooted in the middle of this step, and I was hoping > to present the volumes tomorrow.. ouch. > - > Josh >

Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

no, sorry :< On Mon, 16 Jul 2012, Joshua Lee wrote: > Is it possible/pracitcal? This is a long step, and unfortunately my analysis > computer was rebooted in the middle of this step, and I was hoping to > present the volumes tomorrow.. ouch. > - > Josh > > > _

Re: [Freesurfer] ROI functional & anatomical cross

Hi Doug, Thank you, I think that will work. Right now my anatomical ROIs are in subject native space and I would like to register the third-level group (across subject) fmri activation map to subject native space as well before crossing the two. Is that possible? I have the anat2exf.register.dat f

[Freesurfer] Restart from somewhere in the middle of mri_ca_register

Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] plotting cortical parcellation surfaces using 2009 atlas

Hi Maria you can use the file menu to load the parcellation (file->label->import annotation or something like that), then use the file browser to select the one you want. cheers Bruce On Mon, 16 Jul 2012, Maria Kharitonova wrote: > Hello, > > I apologize if my question is too basic, but I a

[Freesurfer] plotting cortical parcellation surfaces using 2009 atlas

Hello, I apologize if my question is too basic, but I am trying to pull up cortical parcellation surfaces for my data, like shown here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation I tried typing in "tksurfer subjec_number lh inflated -aparc", but that produces the lateral sur

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

can you send us an example? In the ones we've looked at the older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Well, I am using version 5.1.0. I have had sa

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that? -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.

Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

There is not an easy/good way to handle this situation. The way it works is that it goes through each point in the source and finds the closest vertex in the target. If the target is more densely sampled, then there are some points in the target in the middle of the label that are not the close

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi Ayaz what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2) cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All,   After running recon-all, I noticed several subjects that sum of WM

[Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The inf

Re: [Freesurfer] parcellations to fmri space

So you want to make a particular label bigger (more surface area) on cortex? doug On 07/16/2012 02:51 PM, Christopher Bell wrote: > > I tried using mri_label2vol with --aparc+aseg instead of --aparc. This > works and provides cortical and subcortical with no overlap. It doesn't > allow me to do c

Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

Hi, just wanted to bump this up since it looks like Doug is back. On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom wrote: > Hi, > > I'm using mri_label2label to reverse normalize labels from fsaverage > space to the native surface. > > I'm ending up with some splotchy-looking labels, for lack of a

Re: [Freesurfer] parcellations to fmri space

I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks. Chris On Mon, Jul 16, 2012 at 9:0

Re: [Freesurfer] the make_average_subject without aparc.annot

I don't remember what I sent out before, but you can try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface doug On 07/11/2012 03:37 PM, Leon wrote: > Hi, Doug > > I found from the archive that you made a version of > make_average_surface without the

Re: [Freesurfer] ROI functional & anatomical cross

You can create a binary mask of the ROI, then use mri_mask to mask out the non-ROI part from the fMRI. does that work? doug On 07/11/2012 11:25 AM, Huiting Liu wrote: > > Hello, > > > I'm trying to do an ROI analysis that crosses the group-level > functional activation with specific anatomical s

Re: [Freesurfer] Clusterwise correction for multiple comparisons

It does not seem like it should take that much time. You might try this program ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mcsim.linux This is what I use to create the cached results that we distribute. You can use the cached results unless you have a different mask. If y

Re: [Freesurfer] annot 2 label file conversion

Can you send your command line and the full terminal output? doug On 07/11/2012 09:39 AM, Bruce Fischl wrote: > Hi Arnaud > > this question may need to wait for Doug to return. If you don't get an > answer in a couple of days try reposting, and please include your > exact command line and screen

Re: [Freesurfer] Repost: fsgd file

That contrast is correct. If you run mri_glmfit-sim, it will extract the data for each subject and cluster and save it in a text file in the contrast directory. It is better to do it this way instead of mapping the ROIs back to the individual. Look at mri_glmfit-sim --help doug On 07/16/2012 12

Re: [Freesurfer] Coordinate Transformations

Have you looked at this page http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug On 07/16/2012 12:43 PM, jmd33 wrote: > > Hi, > > I'm working on a project project comparing the cortical thickness in > epileptic patients to the corresponding brain area of a control > subject. To do

Re: [Freesurfer] ROI from left to right hemi - cortical thickness

that looks right except "--surfreg sphere" should be "--surfreg fsaverage_sym.sphere.reg" Where did you get those instructions? Did I send them out before? doug On 07/16/2012 01:32 PM, Irene Altarelli wrote: > Dear Doug, > > thanks for your answer. I guess I got confused by the output of the > in

Re: [Freesurfer] ROI from left to right hemi - cortical thickness

Dear Doug, thanks for your answer. I guess I got confused by the output of the interhemispheric registration. So, to be sure I understood correctly: are you suggesting that I should 1) run mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel $SUBJECT_DIR/suj1/label/lh.mylabel.la

Re: [Freesurfer] Repost: fsgd file

Hi Doug, Thanks for your reply. Both scores are on the same scale (z-transformed). But I would like to see whether there is a differential effect on cortical thickness. Do you think the contrast I defined was correct? And do I understand it correctly that what you suggest is the following: warp

[Freesurfer] Coordinate Transformations

Hi, I'm working on a project project comparing the cortical thickness in epileptic patients to the corresponding brain area of a control subject. To do this, I have been trying to transform the patient RAS coordinates to talairach coordinates and then transforming the talairach coordinates int

Re: [Freesurfer] mri_glmfit

Hmmm, that is strange. It's the same error as my previous email. Can you verify that the file below exists and that you can read it? /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd On 07/12/2012 04:28 PM, Jenny Liu wrote: > Hello > > I typed i

Re: [Freesurfer] qdec - ERROR: CSDread():

Does /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd exist and do you have read permission? doug On 07/10/2012 09:20 AM, Natalia h wrote: > Dear expert, > > I got an error while clicking the Monte Carlo simulation in qdec. > I am using Mac 10.6 and qde

Re: [Freesurfer] Flip brain

Hi Tadeu, I have updated the files. The only difference is that the "mcc" file below is now ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz doug On 07/10/2012 09:25 AM,

Re: [Freesurfer] Repost: fsgd file

Hi Heidi, how exactly do you want to draw a conclusion? The slopes for the different variables may be very different because the variables have a different scale. tksurfer scatter plot is made to look at a cortical variable vs a continuous variable. If you want to look at a scatter plot of your

Re: [Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c

Thanks Doug! New version of mri_segstats is working fine for images with small voxels (<1mm3). --Masaya On 07/16/2012 09:43 AM, Douglas N Greve wrote: > Hi Masaya, you are correct. I've put a new version here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux > C

Re: [Freesurfer] Measuring total cortical volume

In the aseg.stats file, there will be these values # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 218425.204942, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 212261.052152, mm^3 # Measure Cortex, CortexVol, Total cortical gray

Re: [Freesurfer] How to register FLAIR to T1?

Often with FLAIR there is not enough gray-white contrast to run the registration. Try using the pial surface instead, with "-surf pial --t1" This tells it to use the pial surface as a boundary. The --t1 is needed because the intensity should go from bright to dark. Let me know if that does not

Re: [Freesurfer] ROI from left to right hemi - cortical thickness

Hi Irene, what are the instructions you are following? If you have mapped the lh.roi to the LH of the xhemi subject (making it the RH), then you can copy it to subject/label/rh.roi and run the normal stats. doug On 07/09/2012 04:31 AM, Irene Altarelli wrote: > Dear all, > > I have a ROI on the l

Re: [Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c

Hi Masaya, you are correct. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux Can you test it out? It also fixes the partial volume computation problem. thanks! doug On 07/06/2012 02:23 PM, Masaya Misaki wrote: > I've posted a questio

Re: [Freesurfer] Ribbon

You can try mris_volmask \ --label_left_white 2 --label_left_ribbon 3 \ --label_right_white 41 --label_right_ribbon 42 \ --save_ribbon $subjid doug On 07/08/2012 01:18 PM, Matt Glasser wrote: > Hi Bruce, > > He just needs the grey matter part of a typical ribbon.mgz volume. H

Re: [Freesurfer] qdec

Hi Carolina, the FWHM is the "full-width/half-maximum" and indicates how much smoothing you have. This is surface-based smoothing, not volume based, and it can be difficult to compare to volume based smoothing as is done in fMRI. The surface-based smoothing can be larger because you don't have

Re: [Freesurfer] multiple correction

On 07/06/2012 10:00 PM, Meng Li wrote: > Hi, freesurfer expert, > I performed the statistical analysis between two groups first in left > hemisphere, and got some regions which showed different. > 1) so if I then do multiple correction, i don't need to run the > mri_glmfit-sim command, and just

Re: [Freesurfer] parcellations to fmri space

Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug On 07/06/2012 12:02 PM, Christopher Bell wrote: > > Hello Freesurfers, > > > I have developed

[Freesurfer] Memory allocation problem trac-all -prior

-- Forwarded message -- From: Rui Lavrador Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 A

[Freesurfer] Repost: fsgd file

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cogni

[Freesurfer] Measuring total cortical volume

Hello, We have a some doubts about how to measure the total cortical volume. Is it recommendable to use GM = pial surface - white matter? Hope to hear from You, Best regards Emelie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail