[Freesurfer] 答复: ROI

Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI can not display on surface(tksurfer patient lh inflated -overlay patient/label/fcd.label ). The terminal showed the following sentence: label stat field identically zero - setti

Re: [Freesurfer] Talairach registration error

the nifti file does not have the needed information in it. where did you get it from? On 9/5/17 8:42 PM, Ariana Vajdi wrote: Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountere

Re: [Freesurfer] Ventricle Volumes Decreasing over time?

Hi Tamara have you visualized the multiple time points of a subject whose ventricular volume is decreasing? How big a decrease are you seeing? cheers Bruce On Tue, 5 Sep 2017, Tamara Tavares wrote: > Hello, > I used the default longitudinal stream to calculate ventricular volumes over > tim

[Freesurfer] Ventricle Volumes Decreasing over time?

Hello, I used the default longitudinal stream to calculate ventricular volumes over time. When I examined the difference score (longitudinal-baseline) I noticed that for some participants ventricular volumes *decreased*. The same site, scanner and scanning protocol was used for both baseline and l

[Freesurfer] Talairach registration error

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

Thank you so much Doug. We're mainly interested in controlling for Sex so it is great to know that it does work for DOSS. Best, Fred > On Sep 5, 2017, at 18:07, Douglas N Greve wrote: > > For DOSS, It will work, but harder to set up the contrast matrices to > look at a sex effect. I would ju

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

For DOSS, It will work, but harder to set up the contrast matrices to look at a sex effect. I would just do it coding males and females as separate classes and not include sex as a variable On 09/05/2017 06:00 PM, Uquillas, Federico D'Oleire wrote: > Thank you Doug. Is the one that doesn't fail

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

Thank you Doug. Is the one that doesn't fail okay? Best, Fred > On Sep 5, 2017, at 16:57, Douglas N Greve wrote: > > in the one that fails you are including the binary gender as a > continuous variable, which will fail in FSGD. All catagorical variables > need to be coded as classes. see >

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

in the one that fails you are including the binary gender as a continuous variable, which will fail in FSGD. All catagorical variables need to be coded as classes. see https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote: > Dear Doug,

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

Dear Doug, Sending the FSGD described in our original email as failing due to it being "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt". The other one is the one that runs and gives expected results with a DOSS contrast [0 1 0

[Freesurfer] Error with TRACULA using dcm and nii

Hi Freesurfer Team!. We are trying to use TRACULA to analyze the structural connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run the tutorial data without any problems but encounter errors when using our own data. We ran recon-all on all of our subjects without any probl

Re: [Freesurfer] sub-cortical analysis

I've added a voxel-based analysis to the wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer Note that I'm recommending using permutation instead of GRF for correction of multiple comparisons On 08/29/2017 10:03 AM, John Anderson wrote: > > Hi Dr Greve, > > I am using pet surfer to an

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

can you send the fsgd file for the analysis that is failing? On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote: > Dear FreeSurfer experts, > > We have run a vertex-wise analysis regressing a continuous variable > onto cortical thickness on the surface, and would like to verify that > ou

Re: [Freesurfer] Cortical thickness

You need to map them into the same space. You can use mris_apply_reg to map one subject into the other or you can use mris_preproc to put them both into fsaverage space On 09/01/2017 10:29 AM, Esteban, Eva(GE Healthcare) wrote: > > Hello everyone, > > I am trying to compare the difference in co

Re: [Freesurfer] R: Re: Map of covariance

you would need to create a contrast to look for the interaction. If you have four gruops and 1 covariate, then it would be 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 On 09/05/2017 04:32 PM, std...@virgilio.it wrote: > Hi, > e.g., by considering two or more groups, I would like to map

Re: [Freesurfer] MNI average brain in Freesurfer space

not sure what you mean, but check out the use cases here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 09/05/2017 03:35 PM, Anna Kasdan wrote: > Hi everyone, > > Is there a freesurfer file/file format for the /average/ MNI brain (as > opposed to fsaverage which is just based on

[Freesurfer] R: Re: Map of covariance

Hi, e.g., by considering two or more groups, I would like to map the clusters reporting the covariance between the functional connectivity or cortical thickness (dependent variable) and age, tacking in account the group differences. Instead, I'm not interested to map the group differences, taki

[Freesurfer] MNI average brain in Freesurfer space

Hi everyone, Is there a freesurfer file/file format for the *average* MNI brain (as opposed to fsaverage which is just based on different subjects)? Or is there a way to turn MNI coordinates into freesurfer space? Thanks so much! Anna Research Assistant, NYU __

Re: [Freesurfer] Problem with ambiguous voxels?

really? I've never seen that. If you upload one of the subjects to our ftp site (the entire subject dir tarred and gzipped) I will take a look cheers Bruce On Tue, 5 Sep 2017, Del Re, Elisabetta wrote: Dear FS Team, We are running recon-all for a large dataset and 5 of the cases keep getti

Re: [Freesurfer] Reliability of labeling procedure in the same scan

I've run many hundreds of scans repeatedly and found variance between versions of FreeSurfer, but identical output within a version. Something must have changed between runs. Perhaps you could try comparing the log files and see where the deviations begin. Mike Schmidt On Sep 5, 2017 10:54 AM, "

Re: [Freesurfer] Fixed Effects Analysis on Single Subject's Brain

Do you mean in the native fMRI space or the native subject surface space? On 09/05/2017 12:15 PM, Taylor, Johnmark wrote: > Hello, > > Quick question. If I scanned a single subject across several sessions > and want to do a fixed effects analysis on that subject's brain > (without registering t

Re: [Freesurfer] individual mri_segstats waveforms for vertices or face in label

You could do it in matlab, something like waveforms = fast_vol2mat(MRIread('waveform.nii.gz')); % this will be a matrix ntimepoints by nvertices You can then load the label with read_label.m and then pull out the columns from waveforms that you want. Make sure to account for the fact that the

Re: [Freesurfer] Combining Echo Frames Error

the first question is whether this is multi-echo data? Assuming it is, you can mv 001.mgz multiecho.mgz mri_concat --rms multiecho.mgz --o 001.mgz On 08/31/2017 09:16 AM, Maksimovskiy, Arkadiy wrote: > > Dear Freesurfer experts, > > Here are the commands I entered, and errors I received: > > r

Re: [Freesurfer] How to estimate the Intracranial area?

do you mean the surface area of the inside of the skull? We do not segment the skull, so no such area measure is possible. On 08/30/2017 11:14 PM, Zhiliang Long wrote: > Dear FS experts: > > I'am writting to ask for help about intracranial area. I can find > the information of intracranial

Re: [Freesurfer] Occipital Cortex Segmentation

On 08/30/2017 03:57 PM, Torrado Carvajal, Angel wrote: > Hello, > > I need to get the segmentation of the occipital cortex. I am > attempting to generate the corresponding ROI, using the > mri_annotation2label command and then running mris_anatomical_stats to > merge the labels and get the act

Re: [Freesurfer] Freesurfer Preliminary Questions

you have to create the directory before you can cd to it. If you don't know how to create a directory in unix, then you should take some time to learn unix before trying to run FS. On 08/31/2017 12:22 PM, Ledesma, Jason wrote: > > Hi Bruce, > > > Do you have any suggestions as to how to determi

[Freesurfer] Fixed Effects Analysis on Single Subject's Brain

Hello, Quick question. If I scanned a single subject across several sessions and want to do a fixed effects analysis on that subject's brain (without registering to MNI or Talairach space), how do I go about doing this? I am trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an o

Re: [Freesurfer] Map of covariance

I don't understand what you are asking. can you elaborate? On 08/30/2017 12:50 PM, std...@virgilio.it wrote: > Hi list, > by applying a design e.g. 4GV1 in fsgd I could assess the dependence > of group differences taking in account the effect of covariate. > Anyway, where I should look if I want

Re: [Freesurfer] upsampling ?h.curv

You can also run mris_apply_reg --src lh.curv --streg lh.white lh.white.upsampled --trg lh.curv.upsampled.mgh On 08/30/2017 01:17 PM, Bruce Fischl wrote: > ?h.curv is just the spatially smoothed ?h.white.H. If you specify -a 10 > (average 10 times) it should be pretty close th ?h.curv > > On We

Re: [Freesurfer] patch for ribbon mgz failure

Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats) https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote: > Hi freesurfer te

[Freesurfer] Problem with ambiguous voxels?

Dear FS Team, We are running recon-all for a large dataset and 5 of the cases keep getting stuck at the exact same spot. It is the point at which the following has just been displayed on the screen: #@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017 mri_segment brain.mgz wm.seg.mgz doing initi

Re: [Freesurfer] Interpretting Brain Segmentation Volume to eTIV ratio

I put that in there mainly as a quality check to automatically flag something that has gone wrong. I think something went wrong if the value is 0.65 (unless you have very atrophied subjects). You will have to take a look to see what might have gone wrong. On 08/29/2017 09:03 PM, Mehta, Chinta

Re: [Freesurfer] group interaction with one continuous covariate and three nuisance variables (two continuous, one dichotomous)

try looking at the FSGD examples for a case that you can generalize https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 08/29/2017 08:59 PM, Ines Mürner-Lavanchy wrote: > > Dear FS experts, > > I would like to test if the correlations between thickness/area and > cognition differ between

Re: [Freesurfer] Multi-Subject Comparison in FreeSurfer

You will need to run 500 different recon-all jobs. Obviously, if you run them on a single computer, it will take a long time, so you will need access to a cluster. Or you can buy time on a cloud service. On 08/29/2017 02:54 PM, Sherrill, John T wrote: > > I am a new grad student and have been a

Re: [Freesurfer] mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."

what is this causing an error in? On 08/29/2017 06:50 AM, Ernst Schwartz wrote: > Hi! > > It seems that in FreeSurfer 6, the comma between “CortexVol” and > “Total cortical gray matter volume” is missing > > here’s the relevant part of one of my stats-files: > > # Table of FreeSurfer cortical pa

Re: [Freesurfer] time.dat file in Kinetic Modelling MRTM1 step - Petsurfer processing

It is just a text file with the time at the middle of the frame. I've attached an example. The time units should be in seconds. On 08/27/2017 11:28 AM, M Janani wrote: Hi team, Could anyone please tell how to create the time.dat file in the Kinetic Modelling MRTM1 step mri

Re: [Freesurfer] Freesurfer PIB PET image processing

the explanation is on this page http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer On 08/27/2017 05:22 AM, M Janani wrote: > Thanks for your reply Douglas. > > Below is the data I have in my gtm.stats.dat file. > >12 Left-Cerebral-White-Matter wm138789 > 65391.64

Re: [Freesurfer] preproc-sess

On 08/31/2017 11:47 AM, Jiahe Zhang wrote: > Dear Freesurfer experts, > > I have two questions regarding preproc-sess: > > 1) What is the default algorithm that does the functional-anatomical > registration? And is there any way to change the default to other > types of registration methods? it

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Right, I think this is a new file with version 6. On 08/31/2017 04:32 PM, John Anderson wrote: > Thank you Dr Bruce, > It seems that FS5.3 doesn't output this file. I just checked many > recons processed using FS5.3 without FLAIR and the file > "aparc.DKTatlas+aseg.mgz" is missing in all these

Re: [Freesurfer] Contrast matrix for PVR

On 08/31/2017 02:30 PM, Martin Juneja wrote: > Hi experts, > > I have a follow up question: > In case I wanted to add another covariate in contrast matrix e.g. in > addition to age and gender if I want to add BMI as another covariate > in calculating correlation between volume and LGI (as menti

Re: [Freesurfer] Reliability of labeling procedure in the same scan

no, I don't think so. There is some randomness in the algorithm (e.g. sampling paths through the volume), but I thought we used the same random seed each time to ensure repeatability. Was it on the same machine? What was your command line? And How big were the differences? On Tue, 5 Sep 2017,

Re: [Freesurfer] Reliability of labeling procedure in the same scan

I mean the hippocampal volume in the aseg... so, it's not normal? Bruce Fischl Sat, 26 Aug 2017 11:24:44 -0700

[Freesurfer] Fwd: Postdoctoral Position Available at Cincinnati Children’s Hospital Medical Center

Postdoctoral Position Available at Cincinnati Children’s Hospital Medical Center, Perinatal Institute The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is seeking a creative and highly motivated individual with solid training in image processing, computer science, and/or neurosc

[Freesurfer] Fwd: Research Associate Position Available at Cincinnati Children’s Hospital

Research Associate Position Available at Cincinnati Children’s Hospital Medical Center, Perinatal Institute The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is seeking a creative and highly motivated individual with solid training in image processing, computer science, and/or n

Re: [Freesurfer] Question on surface-based analysis

Hi Chintan (a) yes, I would think fsaverage would be fine in this age range (b) we do *not* resample into talairach coords, so volumes and surface areas should include eIV or something equivalent as a covariate. Thickness shouldn't require it. cheers Bruce On Tue, 5 Sep 2017, Mehta, Chin

Re: [Freesurfer] Question on surface-based analysis

On 9/5/17 9:09 AM, Mehta, Chintan wrote: Dear FreeSurfer users, I am new to surface based analysis in FreeSurfer (version 6.0). My data consists of T1-weighted scan from normally developing youth of 8 to 21 years of age. I have two questions on assumptions of this analysis for pediatric d

[Freesurfer] Question on surface-based analysis

Dear FreeSurfer users, I am new to surface based analysis in FreeSurfer (version 6.0). My data consists of T1-weighted scan from normally developing youth of 8 to 21 years of age. I have two questions on assumptions of this analysis for pediatric data: (a) Is "fsaverage" an appropriate common