Re: [Freesurfer] V1 Atlas ( brodman maps)

You will need to run mri_aparc2aseg. This is how aparc+aseg.mgz is created (see recon-all.log file for command). Is the V1 a label or an annotation? If label, then you will need to convert it to an annotation (mris_label2annot) On 5/13/16 6:28 PM, John Anderson wrote: Dear Experts, I want t

Re: [Freesurfer] New to Freesurfer; cortical thickness

run them separately On 5/26/16 11:01 AM, Marja Caverlé wrote: Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé mailto:marja.cave...

Re: [Freesurfer] Cluster-wise correction error with mri_glmfit-sim

Instead of --2spaces, use--bonferroni 2 On 5/26/16 10:30 AM, Hao wen wrote: Hello: Freesurfers, follow the tutorial ' # FsTutorial # GroupAnalysis

Re: [Freesurfer] request for corrected p-values for mni305 space

What do you mean? There is a way to correct with mri_glmfit-sim using the --grf option. On 5/25/16 9:25 PM, Joseph Dien wrote: Hi, just a user request for corrected p-values for the mni305 space analyses (i.e., sig.voxel.nii.gz files). Thanks! Joe ---

Re: [Freesurfer] New to Freesurfer; cortical thickness

If you don't give it a -s option, the program will not run and there will not be any output On 5/26/16 10:43 AM, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On F

Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters). On 5/26/16 8:56 AM, Clara Kühn wrote: >

Re: [Freesurfer] Stat doubts

I'm guessing that I can just square at it, to obtain R2. When you asked me to divide the beta by sqrt(rvar), is there any place where I can find is this is the correct way to get the

Re: [Freesurfer] vox2ras and vox2ras-tkr

If you can get the voxel sizes and number of rows, cols, and slices, then the vox2ras-tkr is pretty easy to compute. Search our wiki for coordinates. This page will have a power point presentation that includes how to compute it. doug On 3/21/13 10:02 PM, Eric Larson wrote: Does anyone have c

Re: [Freesurfer] denominator of the t-test in fsfast?

Hi Alex, On 3/31/13 7:37 AM, Alex Kell wrote: freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual *c*(X' * X)^-1*c' where X is the stim matrix and c is

Re: [Freesurfer] mri_glmfit-sim doesn't recognize --label flag

Hi Cherry, you need to run mri_glmfit with the --label flag. Then run mri_glmfit-sim without a label flag. mri_glmfit-sim will see that you used a label and incorporate it. doug On 3/30/13 7:02 PM, Yizhou Ma wrote: Dear freesurfer experts, I'm doing small volume correction for multiple com

Re: [Freesurfer] FS 5.2 asegstats2table is not found or is too small to be a valid stats file error

does that file exist? On 3/31/13 12:11 PM, Salil Soman wrote: Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PA

Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces

When you say it does not work, what do you mean? Did it not put the label in the right place? The number of vertices in the output label may be much less than in the input. label2label just finds the vertex that is closest to each label point. A multiple input label points may map to a single

Re: [Freesurfer] Bad Talairach Registration

Hi Cherise, the multiple frame error hints to some issue with the data. It means that it has multiple images, like an fMRI volume (which will not work), but it could be multiecho mprage (which would be ok after computing RMS). What are you using as input? doug On 4/3/13 10:23 PM, Cherise R.

Re: [Freesurfer] merging dti data

Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: > we captured some dti data. there were 2 runs. we acquired in the axial plane, > 2mm slice thickness the first run captured the lower half of the b

Re: [Freesurfer] merging dti data

ine for merging two > whole brain datasets. > jon > > - Original Message - > From: "Douglas Greve" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, April 10, 2013 10:13:05 PM > Subject: Re: [Freesurfer] merging dti data > > > Hi Jon, I don&#

Re: [Freesurfer] using volume label mask in mri_vol2surf

Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote: Dear all I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 c

Re: [Freesurfer] using volume label mask in mri_vol2surf

Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask.

Re: [Freesurfer] using volume label mask in mri_vol2surf

urv --projfrac 0.5 and got this error, Writing to ./lh.R2MaskBrain Dim: 152308 1 1 MRIwriteType(): code inconsistency (file type recognized but not caught) ERROR: saving ./lh.R2MaskBrain # Bug, or user stupidity??? cheers, Fred On 14 Apr 2013, at 22:56,

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

Hi Corinna, I hate to pass the buck, but I think you'll have to contact the FSL people to get it sorted out. doug On 4/16/13 9:31 AM, Corinna Bauer wrote: Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared object file: No such file or directory. On Fri, Apr 12, 2013

Re: [Freesurfer] QDEC questions

For #2, it is hard to say without seeing the design. I would not say that covariates should not change the results (otherwise one would not add them), especially age. If you have a balanced design, then one would hope that adding age would reduce the residual noise and show more of an effect.

Re: [Freesurfer] A problem while doing retinotopy by freesurfer

Hi Yufeng, it cannot handle only a single run. You must have both polar and eccen. You can "fool" it by copying your polar run into another run and calling it eccen. doug ps. Please remember to send email to the list and not to me personally. Thanks! On 4/16/13 11:02 AM, yuf...@mail.ustc.edu.

Re: [Freesurfer] cwpvalthresh not specified

yes, correct On 4/23/13 11:05 PM, Jeni Chen wrote: Hello, Just a quick question, if the 'cwpvalthresh' flag wasn't specified when running mri_glmfit-sim, the script will use the default .05 value, correct? Thanks for clairfying. Jeni Chen

Re: [Freesurfer] System recommendations for Freesurfer

I think Nick meant to say 400MB per subject, not 400GB per subject:) On 4/24/13 8:42 PM, Nick Schmansky wrote: > Graham, > > Hi, to answer each: > > Intel vs AMD: no preference. also, CPU speed is not critical. Its > better to have at least 4GB, and budget 4GB per subject you want to > proce

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

Hi Jeni, done pass that path to the csd, just the csd base. In your case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS doug On 4/24/13 8:47 PM, Jeni Chen wrote: Hello, I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 110, Issue 20

Hi Rotem, I don't think I ever got an email notifying me. Did you use www.nmr.mgh.harvard.edu/facility/filedrop/index.html ? Can you upload it again, and make sure to put my email in the contact list. doug On 4/29/13 9:08 PM, Rot

Re: [Freesurfer] convert labels to volumetric masks

Hi Meng, I don't know anything about that atlas. What space is it in? And how did you process the functional data? On 5/1/13 9:14 PM, limengsecret wrote: > > > Hi Doug, > > > The relative freesurfer files were downloaded from > http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

Bruce, did you ever write something that automatically makes cuts based upon the aparc? I think Bilal is also looking for something like that. doug On 5/2/13 9:31 PM, Bruce Fischl wrote: > Hi Bilal > I think I wrote something called label2patch or label2flat for this propose. > Let me know if

Re: [Freesurfer] Using mri_cor2label

yea, the aseg only goes to 255. On 5/3/13 10:44 PM, Bruce Fischl wrote: > Hi Jeff > Don't you want the aparc+aseg not the aseg? > Bruce > > > > On May 3, 2013, at 10:37 PM, jwa...@nmr.mgh.harvard.edu wrote: > >> Thanks Doug, >> >> The command line I am running is: >> mri_cor2label --c >> /clus

Re: [Freesurfer] question about glm setup

Hi Subha, yes, you can. You will need to create a table in the format with QDEC expects. Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis doug On 5/4/13 11:31 AM, Subhabrata Chaudhury wrote: Hi, I am new to freesurfer. I have run recona

Re: [Freesurfer] BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)

Newer version of linux changed the way cshell behaves which causes bbregister to crash in some instances. Get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/6/13 8:10 PM, Todd Thompson wrote: > Hi, all. I'm trying to refine my pial

Re: [Freesurfer] ICV

It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage 23:724-738. "Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align

Re: [Freesurfer] Look-up table for aparc+aseg

try $FREESURFER_HOME/FreeSurferColorLUT.txt doug On 5/8/13 8:22 PM, Chang, Yishin wrote: Hi, Sorry if this is a duplicate question, but I can't find the answer anywhere. Where can I find a comprehensive look-up table for the indices in aparc+aseg? I'm using version 5.1.0. If a comprehensive

Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

Hi Glen, can you give us more information about what you did? Eg, command line? doug On 5/8/13 8:53 PM, Glen Lee wrote: Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2sur

Re: [Freesurfer] Working with MEMPRAGE

the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: > Hi Kayle > > you would run recon-all on the RMS, then run the dura stuff posthoc. > > cheers > Bruce > On

Re: [Freesurfer] Correction for multiple comparisons question

Hi Panagiotis, On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote: > Hi Freesurfer experts, > > I was wondering about three things concerning the use of the mri_glmfit-sim > command: > > 1) I tried running it with the --2spaces flag in order to Bonferroni correct > over the two hemispheres but it te

Re: [Freesurfer] Restricting ROI Analysis

Hi Skyler, I don't think we have the ability to restrict the analysis to an ROI in QDEC. You can do it with mri_glmfit with the --mask or --label option. doug On 5/12/13 4:25 PM, Skyler Gabriel Shollenbarger wrote: > Hi everyone, > > We are trying to restrict an analysis using Qdec to a region

Re: [Freesurfer] Binary volume to surface label

It cannot create a label file directly. What happens when you try to load it as an overlay? Make sure to set the threshold to 0.5. Also, before going to the surface load the binary volume onto the anatomical with the surfaces to make sure that the surfaces pass through the mask. doug On 5/1

Re: [Freesurfer] thickness

On 5/11/13 7:41 PM, Tudor Popescu wrote: Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while fact

Re: [Freesurfer] Usage of --area option in estimating the vertex-wise maps of surface area

Hi Xi-Nian, it does not do the same thing, but it does something similar. Anderson found that it gave similar results in a lot of cases, but he has found some differences. If he's still following the FS list, maybe he can comment. doug On 5/11/13 9:53 PM, Xinian Zuo wrote: Hello Doug,

Re: [Freesurfer] Freesurfer hemisphere surface flipping

Hi Hamza, have you seen this page? http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi doug On 5/16/13 5:11 PM, Hamza Alshuft wrote: Dear Freesurfers and experts Does anyone know how to flip hemisphere surfaces (cortical thickness) for with-in group analysis? I am analysing a cohort of unilateral

Re: [Freesurfer] T or Z values in QDEC

Hi Philip, the p-value for the cluster is not computed from a t or z. It is computed from a simulation in which random noise is generated on the surface, smoothed, clustered. The maximum cluster size is found. This is repeated 1 times to give a list of 1 cluster sizes. The p-value for a

Re: [Freesurfer] Peak coordinates & Paired t-test with QDEC

Hi Jamie, On 5/24/13 7:18 PM, Jaime Ide wrote: Dear Freesurfer experts: I have two questions: 1) How can I obtain the _peak coordinates_ and _the size_ of the _clusters_ (with uncorrected threshold) visualized in *tksurfer*? (like the tables generated with glmfit-sim) not from tksurfer. You c

Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34

yongxia, did you see my reply from yesterday? On 5/24/13 6:08 PM, Douglas N Greve wrote: > where did your raw data come from? Specifically, how were the nifti > files created? There is a warning in there that indicates that there > is some problem with them. > doug > > > On 05/24/2013 05:56 PM,

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

ats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Hi Sal, yes you can. Use bbreg

Re: [Freesurfer] Correction for multiple comparisons error

what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: > Hi! > > I have been running the mri_glmfit-sim command to do the correction for > multiple comparisons for my group analysis and for some voxel-based

Re: [Freesurfer] BBR Register failing

this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Sal

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

gister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

olume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

It is based on the white. Notice that since you are using an average subject (fsaverage6) there is some scaling that happens because an average subject will have a surface area that is much less than the average of the subjects that went into. The average of the subjects is kept when the avera

Re: [Freesurfer] mri_glmfit files

Look at mri_glmfit --help. The only one not explained there is cnr.mgh which is the contrasts (gamma) to residual noise stddev (rstd.mgh in the glmdir) doug On 5/27/13 4:48 AM, Joshua deSouza wrote: Hello all, I would just like to know what is the significance of the files that are produc

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

If FSL is not installed, then bbregister should have failed and recon-all should have stopped. Did that not happen? To answer your question, it might not make any difference. If the flair and T1 were acquired at the same time, then it probably just used the scanner coordinates to do the init

Re: [Freesurfer] white matter volume per lobe...

you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

-save-reg --reg register_bold.dat" (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space? yes Thank you for all of your help. Best wishes, Sal On Mon, May 27, 2013 at 7:23 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: On 5/26/13

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

I think it depends on how you do the computation. You would probably weight each vertex by the area then sum then divide by the total area and this is probably not much different than just averaging over vertices without taking the area into account. doug On 5/29/13 9:16 AM, Martijn Steenwij

Re: [Freesurfer] SUMA and FSFAST

sorry, I've never used SUMA. Maybe Ziad can chime in (though he's probably never used FSFAST!) doug On 5/28/13 8:57 PM, Joseph Dien wrote: I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use

Re: [Freesurfer] head motion values

fmcpr.mcdat are the motion estimates (mm and degrees). mcprextreg is the motion correction parameters after analysis using a PCA, which is why there is such a huge difference. By default we use the top 4 components. doug On 5/28/13 8:28 PM, Joseph Dien wrote: I have a follow-up question for

Re: [Freesurfer] beta weights from FS-Fast analysis

On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signa

Re: [Freesurfer] mris_divide_parcellation color table error

Tina, what version of FS are you using? At one point I fixed a bug that caused the color to be non-unique, but I don't think the problem looked that bad. If this is the program I fixed, then I'm pretty sure that it would have been in by 5.2. doug On 5/29/13 9:01 PM, Bruce Fischl wrote: hmmm,

Re: [Freesurfer] Conversion

Anna, if you need to get it back into the native anatomical space, see http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat You can use nii as the output format instead of mgz doug On 5/31/13 7:23 AM, Anna Josefson wrote: Dear FreeSurfer users! I am new to Freesurfer, and I have s

Re: [Freesurfer] Cortical thickness

This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug On 6/2/13 3:57 AM, Joshua deSouza wrote: Hi Doug, This file that your saying, will be created after glmfit-sim is done using the cache fun

Re: [Freesurfer] Cortical thickness

on my questions if they seem a little trivial) Thank you Joshua On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should alw

Re: [Freesurfer] Cortical thickness

in the area around the hippocampus and parts of it are being left out in the mask, such as the para-hippocampal region. Regards Joshua On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: The residual FWHM is measured from the data itself. You

Re: [Freesurfer] use of anot_2_label

brainstem is not part of cortex. Use mri_cor2label with the aseg. get the id from $FREESURFER_HOME/FreeSurferColorLUT.txt doug On 6/3/13 6:17 AM, LAOUCHEDI MAKHLOUF wrote: Hi i used mri_annotation2label to extract the cortical labels. for this command we must specify which hemisphere

Re: [Freesurfer] Group Analysis Question

I would not expect them to be identical but similar. If they change a lot there may be an issue with your data. doug On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote: > Hey Doug, > > I have run a group analysis on my data with two different ways. (The input is > cortical thickness.) In the fir

Re: [Freesurfer] mri_glmfit-sim error

hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simul

Re: [Freesurfer] Monte Carlo simulation

what do you mean by the real value of p? On 6/5/13 10:17 AM, std...@virgilio.it wrote: Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p<0.05. Is possible to obstain form each significant cluster the real value of

Re: [Freesurfer] volume called 001.mgz

Hi Varghese, is Image1 a dicom file? doug On 6/10/13 10:09 AM, Varghese Chikku wrote: Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for Free

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstat

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

segmentation 0 1 81837 81837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Doug

Re: [Freesurfer] License problem

Hi Claus, I have never seen this before. Maybe Zeke has an idea? doug On 6/11/13 5:02 AM, Claus Svarer wrote: Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands:

Re: [Freesurfer] OptSeq2 eff and first order and contrast

On 6/13/13 9:45 AM, A a wrote: Hello all, A question regarding the usage of Optseq2 I have this command line optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev ev40 2.5 20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o OptSeq_TRIALS/3_null9_6 --nsearch 1 No

Re: [Freesurfer] Doubts on bblabel

you have to chose it yourself doug On 6/13/13 6:04 AM, Anupa AV wrote: Dear FS experts, By definition bblabel means.. Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the

Re: [Freesurfer] reg-feat2anat failure..

Does that file exist? Do you have permissions? doug On 6/12/13 12:59 PM, Sudhin A. Shah wrote: Hi, recon-all was successful. But when I try reg-feat2anat --feat '/home//func/2_reg' --subject xyz I get an error with MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): c

Re: [Freesurfer] Visualizing functional maps in tksurfer

or you can convert the label to a mask, then run mri_mask on he sig.nii.gz file, then view it in tksurfer. Bruce's suggestion is probably easier. doug On 6/13/13 1:04 PM, Bruce Fischl wrote: > Hi Resa > > you can create a label of the region you are interested in and use the > mask_label comman

Re: [Freesurfer] Fwd: Talairach Positioning in Horizontal View

Did it change anything at all? Make a copy of the talairach.xfm file, re-run, and see if it is different in any way. doug On 6/13/13 1:06 PM, Peter Boulos wrote: Hi Doug, I am using a GE 3T scanner with a slice thickness of 1.7 mm. I tried using the new script you provided (thanks for the he

Re: [Freesurfer] pvr help

Hi Prapti, can you send the full terminal output? The ill-conditioned error is probably not related to the contrast. It is usually related to the design matrix, which makes it difficult to track down because you will have a different one at each vertex with --pvr. doug On 6/13/13 1:14 PM, Ga

Re: [Freesurfer] Xhemi question

Hi Daria, this is not something you would do with tkregister. First, you need to map the curvature from the individual subject to fsaverage_sym. You can do this for all subjects in your group with a call to mris_preproc; spec --meas curv instead of --meas thickness. Then load this as an overla

Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess

It is not a matlab problem per se, though their memory management is not great. This sometimes happens for the mni305 when you have a lot of time points in one run or many runs. How many runs and how many time points per run? And you are doing 2mm (the default) or 1mm? doug On 6/13/13 2

Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess

It does not matter if the paradigm files have events that are before the start of the "run" or after its end. doug ps. Adding more memory would fix it, but I don't know how much you would need to add On 6/13/13 4:29 PM, Marcel Falkiewicz wrote: Hello Doug, I've got o

Re: [Freesurfer] versus baseline in mkcontrast-sess

No, no difference doug On 6/13/13 3:56 PM, Reza Rajimehr wrote: > ... and one more question: > > In the latest version of FS-FAST (v5.3), is there a difference between the > following two: > > mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 -c 0 > > mkcontrast-sess -analysis whatever -co

Re: [Freesurfer] Installing optseq2!!

You will need to make sure it is executable by running chmod a+x optseq2 You then need to put it in your path, rehash, and it should run. Also, if you have freesurfer installed, then it should be there already doug On 6/13/13 5:10 PM, fMRI wrote: > Hi all, > > I am trying to install optseq2 in

Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess

Good idea. Actually, I need to fix selxavg3-sess to handle this better. When I wrote it, I never tested it on runs with so many time points, but they are becoming more common. doug On 6/13/13 5:26 PM, Marcel Falkiewicz wrote:

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Hi Tudor, the lGI stream definitely uses matlab, so that will be a problem at some point if not now. I would have thought that it would have reported that it could not find matalb. Marie would know for sure. doug On 6/14/13 3:25 AM, Tudor Popescu wrote: Dear Freesurfer & localGI experts,

Re: [Freesurfer] Help with QDEC error

Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age,

Re: [Freesurfer] SPM ROI to Cortical Thickness

I don't know anything about XjView. You will need to be very specific and detailed about what you did in order for us to help you. Eg, what space is the ROI in? doug On 6/15/13 8:40 AM, xiangbo_2010 wrote: Dear experts, I was wondering if anyone can advise on the best way to use an ROI

Re: [Freesurfer] problem bbregister onto longitudinal pipeline

Hi Daniel, "fails completely" is not very informative. Can you send the bbr log file? doug On 6/14/13 3:25 AM, Daniel Garcia wrote: > Dear Freesurfer Users, > > I'm having a problem to register my PET images into the longitudinal > pipeline of freesurfer (version 5.1). > > I have use bbregiste

Re: [Freesurfer] Converting fsaveraged EPI to volume

Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug On 6/14/13 10:32 AM, Marcel Falkiewicz wrote: Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like t

Re: [Freesurfer] Group Analysis Error

Hi Nooshin, you can't do a statistical analysis with two data points. The you could look at a simple difference in the time points. If you have two time points for other subjects, you could get means and stddevs from them and compute a z-score of the change for you subject. doug On 6/12

Re: [Freesurfer] Fwd: Conversion

Hi Anna, if you just want to create a binary mask, you can use mri_binarize --i aparc+aseg.mgz --match 18 54 1035 2035 --o amyg+insula.nii this will give you a binary mask of amygala and insula doug On 6/12/13 10:50 AM, Anna Josefson wrote: Hi again freesurfers, I have some beginner's pro

Re: [Freesurfer] Parameterization Optseq

Hi Donna, on the 2nd command line you need to change --tnullmax to 7 sec to be compatible with the 1st command line. I ran this and it works. doug On 6/11/13 8:45 AM, Laura Dekkers wrote: Dear Doug, Thanks you for your e-mail and sorry for the inconvenience. Here is the code again. In this

Re: [Freesurfer] Optseq - optimal parameters

Hi Ella, On 6/16/13 9:27 AM, Ella Hinton wrote: Hi all, I have been advised to use optseq to aid my event related fMRI design, specifically to help calculate stimulus order and timing. I've read the help in some detail but am still a little unclear on some of the appropriate values to input

Re: [Freesurfer] Converting fsaveraged EPI to volume

: Allocing output Done allocing nframes = 1702 Computing sum across frames Writing to f_vol.nii.gz sob, 15 cze 2013, 21:04:20 CEST vlrmerge done Full log is attached. Marcel 2013/6/15 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> Hi Marcel, vlrmerge should handle multiple fra

Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess

re 3x less memory to process, but it crashes with OUT OF MEMORY message. Best regards,  Marcel 2013/6/13 Douglas Greve <gr...@nmr.mgh.harvard.edu> Good ide

Re: [Freesurfer] Optseq optimizing event design

I would not agonize about getting the maximum possible efficiency. When you go to analyze your data, there will be differences that you cannot control (eg, including motion correction regressors or temporal whitening), and these will change efficiency. The only thing I would change to the comm

Re: [Freesurfer] Fwd: DICOM unpacking error

Luc, it is missing the pixel spacing (ie, voxel size), which is a fundamental quantity which should not be missing. Have you anonymized the data or done something else too it? doug On 6/17/13 2:36 PM, Luc Amdahl wrote: -- Forwarded message -- From: *Luc Amdahl* mailto:luc

Re: [Freesurfer] 回复: SPM ROI to Cortical Thickness

Hi Bo, you should run the MNI152 template through recon-all, then map your mask to the surface, create a label, then map the label to each individual subject with mri_label2label doug On 6/17/13 7:24 PM, xiangbo_2...@126.com wrote: I analysis the volume of grey matter, and MNI152 as the mask

Re: [Freesurfer] nifti1Read(): unsupported slice timing pattern 5

Hi Mariam, I don't know why it does not read this particular code. I can modify it when I get back from HBM and send you a new version of mri_convert. Or you might be able to change the way you convert from BRIK to use a different slice code. doug On 6/17/13 4:13 PM, Mariam Sood wrote: > He

Re: [Freesurfer] problem downloading Xhemi files

Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download

Re: [Freesurfer] Tracula bbr errors

Hi Matt, was I supposed to get back to you on this? I generally leave these types of questions to Nick and Zeke. doug ps. Please post to the list instead of us indivudally. thanks! On 6/16/13 12:46 PM, Matthew Hoptman wrote: > Hi Dr. Greve, > Any news on the libboost_program_options.so.5 issue?

<    4   5   6   7   8   9   10   11   12   13   >