Re: [Freesurfer] number of vertices

usually a bit less than that - aroudn 140K or so >Bruce > >On Mon, 29 Feb 2016, >Yang, Daniel wrote: > >> Hi Bruce, >> >> Is it okay to say that it is approximately 160,000 vertices per >> hemisphere? I found the answer from a paper >> >>(htt

[Freesurfer] number of vertices

Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a fixed number or an approx. number? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@

Re: [Freesurfer] number of vertices

On 2/29/16, 11:42 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >Hi Daniel > >the number of vertices will vary depending on the surface area and >geometry >of the white matter for each hemisphere. > >cheers >Bruce > >

Re: [Freesurfer] mri_convert and image orientation

Just to note for people who are interested: It does seem that when voxel-to-ras determinant > 0, then the file is neurological. -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 1/26/16, 10:09 PM, "Yang, Daniel" wrote: >Thanks so much, I s

Re: [Freesurfer] mri_convert and image orientation

eesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" wrote: >If the determinant is less than 0, then it is radiological (probably it >will be radiological). > >On 01/26/2016 04:20 PM, Yang, Daniel wrote: >> Dear Doug, >> >> Thanks for your reply.

Re: [Freesurfer] mri_convert and image orientation

id that, even if the det<0, it may still show >up funny in fslview > >On 01/25/2016 12:11 PM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> I find that mri_convert will convert DICOM of structural scan to >> neurological orientation by default. >>

[Freesurfer] mri_convert and image orientation

Dear FreeSurfer experts, I find that mri_convert will convert DICOM of structural scan to neurological orientation by default. For example, mri_convert --in_type dicom --out_type mii Thus, the NII may need to be swapped in x for use in FSL. In this the case? Many thanks, Daniel -- Daniel Y

Re: [Freesurfer] TalX TalY TalZ

r.mgh.harvard.edu>> Date: Wednesday, November 11, 2015 at 11:01 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TalX TalY TalZ If you use --fixmni, then they are reported

[Freesurfer] TalX TalY TalZ

Dear FreeSurfer Experts, Are these coordinates reported in mri_surfcluster in MNI305 space? (with —fixmni) Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

Re: [Freesurfer] mri_surfcluster statistics and label question

Greve" wrote: >There should be a t.mgh file there (or maybe F.mgh). You can just pull >the value out of the vertex out of that. > >On 11/9/15 6:46 PM, Yang, Daniel wrote: >> Hi Doug, >> >> Got it! Sorry that I keep forgetting this. So it’s an exponent >>statistic.

Re: [Freesurfer] mri_surfcluster statistics and label question

derive the t-statistic? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 6:02 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" wrote: > > >On 11/09/2015 10:51 AM, Yang, Daniel wrote: >>

Re: [Freesurfer] convert label to mgh

el2label with the --mask option > >On 11/09/2015 01:34 PM, Yang, Daniel wrote: >> Dear FreeSurfer Experts, >> >> Is it possible to convert a label file to a surface-based mgh file? >> Could you please provide an example (e.g., on a white surface)? >> >> Bes

[Freesurfer] convert label to mgh

Dear FreeSurfer Experts, Is it possible to convert a label file to a surface-based mgh file? Could you please provide an example (e.g., on a white surface)? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___

[Freesurfer] mri_surfcluster statistics and label question

Dear FreeSurfer experts, In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), what is the statistics behind the Max? Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-sta

Re: [Freesurfer] Curvilinear interaction with age

mri_glmfit. So just >create those columns, fit and test. Of course you need to make sure that >the order of subjects in Y is identical with the one used in X. > >Cheers, Martin > >On 11/06/2015 06:14 PM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> I

[Freesurfer] Curvilinear interaction with age

Dear FreeSurfer experts, I have a group variable (X) with two levels and I want to test if there is a curvilinear interaction with age (Z). Can this be tested in FreeSurfer? Specifically, the model would be Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error I want to test b5 while controlli

[Freesurfer] aparcstats2table

Dear FreeSurfer Experts, When I perform aparcstats2table —meas area, does it get it pial.area or white area? I believe it is the pial.area, but this is not documented. If yes, what can I obtain white area via aparcstats2table? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mai

Re: [Freesurfer] how to obtain individual's pial_lgi value

Hi all, Found an answer here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html It works for me! Best, Daniel From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Daniel Yang mailto:daniel.yj.y...@yale.edu>> Reply-To: Freesurfer support list mailto

[Freesurfer] how to obtain individual's pial_lgi value

Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] stat/math tools for MGH file

you will be able to use the FSL tools > >cheers >Bruce > > >On Tue, 3 Nov 2015, Yang, Daniel >wrote: > >> Dear FreeSurfer experts, >> >> I have a number of *.cluster.mgh files and I would like to calculate >>their >> difference and peak coordi

[Freesurfer] stat/math tools for MGH file

Dear FreeSurfer experts, I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL. For example, given two images, I want to know the brain regions in image1 but not in image2. Could you please recommend th

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

Thanks so much for your help!! - Daniel On 8/6/15, 3:06 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >ignore grayvol, the other two will be the mean and standard deviation of >the sulc > >cheers >Bruce >On Thu, 6 Aug 2015, Yang,

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >sure, you can use mris_anatomical_stats with the label (-l) and specify >sulc instead of thickness on the command line >Bruce >On Thu, 6 Aug 2015, Yang, >Daniel wrote: > >> Dear Fre

[Freesurfer] how to obtain sulcal depth in a given region for a specific subject

Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] visualize subcortical areas in tksurfer?

subcortical structures you are better off showing the > results in slices. > > cheers > Bruce > > >> On Mon, 23 Feb 2015, Yang, Daniel wrote: >> >> Hi Bruce, >> Thanks for the reply. My main question is how to best visualize subcortical >> activation

Re: [Freesurfer] visualize subcortical areas in tksurfer?

surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to wh

Re: [Freesurfer] visualize subcortical areas in tksurfer?

t; >no, tksurfer visualizes surfaces exclusively, and the subcortical >structures are volumetric by and large. You could tesselate their surface >and view it in tksurfer, or just use tkmediit or freeview. > >cheers >Bruce >On Thu, 19 Feb >2015, Yang, Daniel wrote: > >

[Freesurfer] visualize subcortical areas in tksurfer?

Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] extract individual label from Destrieux Atlas

gt;" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] extract individual label from Destrieux Atlas Use --annotation a2009s.aparc On 2/19/15 8:34 PM, Yang, Daniel wrote: Dear FreeSurfer experts, The following command works but how do I get the labels from —a2009s ? mri_annotation2

[Freesurfer] extract individual label from Destrieux Atlas

Dear FreeSurfer experts, The following command works but how do I get the labels from —a2009s ? mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir . What is the difference between a2005s and a2009s? Thanks! Daniel ___ Freesurfer mail

[Freesurfer] ROI

Dear FreeSurfer experts, I drew a label that crosses the cortical and subcortical boundary. But FreeSurfer still allows me to obtain statistics using this label for a given subject, for example, area, volume, and thickness. I am wondering if these statistics are valid since it crosses cortical

Re: [Freesurfer] mri_label2label results

On Jun 19, 2014, at 10:20 PM, "Bruce Fischl" mailto:fis...@nmr.mgh.harvard.edu>> wrote: Yes, it was only mri_label2label has that bug On Jun 19, 2014, at 10:14 PM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Thanks! Is there a list of bug fixed (aft

Re: [Freesurfer] mri_label2label results

g we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that th

Re: [Freesurfer] mri_label2label results

? Is the difference between 1 and 3 trivial? Thanks! Daniel On 6/19/14, 8:13 PM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On

Re: [Freesurfer] mri_label2label results

t; >Bruce > >On Thu, 19 Jun 2014, Yang, Daniel wrote: > >> Dear all, >> >> I found that mri_label2label generates different results, depending on >> whether the software¹s platform is MacOS Lion or Cent

[Freesurfer] mri_label2label results

Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] subcortical segment NIFTI files

r. I doubt that there will be much practical difference. On 6/17/14 3:08 PM, Yang, Daniel wrote: Hi Doug, Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl And obtained the following: fsaverage 1.00 1.000

Re: [Freesurfer] subcortical segment NIFTI files

gt;" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files I think I just ran something like bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl Maybe I tweeked it manually On 6/17/14 1:10 PM, Yang, Daniel wrot

Re: [Freesurfer] subcortical segment NIFTI files

ot;freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right dire

Re: [Freesurfer] subcortical segment NIFTI files

.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as th

Re: [Freesurfer] subcortical segment NIFTI files

mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted belo

Re: [Freesurfer] subcortical segment NIFTI files

ou are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Tex

Re: [Freesurfer] subcortical segment NIFTI files

.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Th

[Freesurfer] reg.1mm.mni152.dat

Dear all, While there is the file ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no such file as: ${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat or ${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ? I am wondering how we can

Re: [Freesurfer] subcortical segment NIFTI files

or > >Cheers >Bruce > >> On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" >>wrote: >> >> Hi Bruce, >> >> Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very >> flexible. I meant to obtain the aseg individual label

Re: [Freesurfer] subcortical segment NIFTI files

e > >> On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" >>wrote: >> >> Dear all, >> >> While it is possible to obtain NIfTI files for cortical parcellation >>using mri_annotation2label, I am running if it is

[Freesurfer] subcortical segment NIFTI files

Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] Frontal WM volume

nd add up the volumes. If you have another way to define frontal, then you'd have to tell us what that is. doug On 05/14/2014 05:37 PM, Yang, Daniel wrote: Dear FreeSurfer group, If I want to extract frontal WM volume, is it something doable in FreeSur

[Freesurfer] Frontal WM volume

Dear FreeSurfer group, If I want to extract frontal WM volume, is it something doable in FreeSurfer? Much obliged, Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The info

Re: [Freesurfer] MeanThickness

tically includes these measures. Can you check? And, yes, mean thickness can be computed as (lh+rh)/2 doug On 3/30/14 12:58 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three li

[Freesurfer] MeanThickness

Dear FreeSurfer Experts, I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three lines. For example: # Measure Cortex, NumVert, Number of Vertices, 107414, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4,

Re: [Freesurfer] WM vol as measure

the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Ya

Re: [Freesurfer] WM vol as measure

Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 2:17 PM, "Douglas N Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12

Re: [Freesurfer] WM vol as measure

led wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center Ne

Re: [Freesurfer] WM vol as measure

12:58 PM, "Douglas N Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know ho

Re: [Freesurfer] WM vol as measure

Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/2/14 7:18 PM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have

Re: [Freesurfer] WM vol as measure

n 3/2/14 7:18 PM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM reg

[Freesurfer] WM vol as measure

Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel __

Re: [Freesurfer] two labels in tksurfer/freeview?

l" mailto:fis...@nmr.mgh.harvard.edu>> wrote: mri_morphology for the .mgz for the label you can do it in tksurfer in the tools->label menu or use mri_label2label (at least I put it in the dev version, not sure if it is released yet) On Thu, 27 Feb 2014, Yang, Daniel wrote: By the way, wha

Re: [Freesurfer] two labels in tksurfer/freeview?

wrote: that's a good way to do it. You don't even need to save it as an mgz. You can just do tools->labels->copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label->stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote: Than

Re: [Freesurfer] two labels in tksurfer/freeview?

y to do it. You don't even need to save it as an mgz. You can just do tools->labels->copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label->stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote: Thanks for both of you for th

Re: [Freesurfer] two labels in tksurfer/freeview?

code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-st

Re: [Freesurfer] two labels in tksurfer/freeview?

labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is fi

[Freesurfer] two labels in tksurfer/freeview?

Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific st

Re: [Freesurfer] ocn?

nothing may have survived correction or because the threshold was too high doug On 2/21/14 8:47 AM, Yang, Daniel wrote: Dear FreeSurfers, I obtained a file from cluster analysis, called "cache.th20.pos.sig.ocn.mgh" Can you tell me what OCN stand for? And what is this file for? I tried to view

[Freesurfer] ocn?

Dear FreeSurfers, I obtained a file from cluster analysis, called "cache.th20.pos.sig.ocn.mgh" Can you tell me what OCN stand for? And what is this file for? I tried to view it but was unable to see anything. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Stud

Re: [Freesurfer] interpretation of a 3-way interaction

o come up with a sentence like the one you are trying to state doug On 02/20/2014 02:25 PM, Yang, Daniel wrote: Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interac

[Freesurfer] continusous x continuous interaction?

Dear FreeSurfer Experts, In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes the testing of the main effects of two continuous variables. In order to test the interaction effect, I think we can form an interaction term like age x weight as the third covariate,

[Freesurfer] interpretation of a 3-way interaction

Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In fem

Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

mailto:gr...@nmr.mgh.harvard.edu>> wrote: Let's say you have four groups with 10 20 30 40 (100 total). The first group would get a weight of .25 where it only had 10% of the total. I don't think there is any way around this. On 2/18/14 4:07 PM, Yang, Daniel wrote: Doug, sorry,

Re: [Freesurfer] interaction between two covariates in qdec?

Sorry, I've found an answer to this here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32928.html Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/19/14 6:47 PM,

[Freesurfer] interaction between two covariates in qdec?

Dear FreeSurfer Experts, In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it says "Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able." However, I cannot select more than one covariate in qdec. Any suggestion? I'm using qdec in Mac, FreeSurfer 5.3.

Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

: yung-jui.y...@yale.edu On 2/18/14 2:13 PM, "Douglas N Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One fo

Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are

[Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I

[Freesurfer] Interaction test

Dear FreeSurfer developers and experts, If I have a binary factor (Group1: patients, Group2: controls) and a continuous variable (age), I know I can follow Contrast2 in the following wiki to test the interaction effect. http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Contrast2: [0 0 1 -1

Re: [Freesurfer] one factor with three levels in qdec?

the wiki for more details. doug On 2/16/14 4:53 PM, Yang, Daniel wrote: Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified.

[Freesurfer] one factor with three levels in qdec?

Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y … I am wondering if th

[Freesurfer] MPRAGE SNR

Dear FreeSurfer Experts, Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ? For examples, I read that SNR is improved in multiecho MPRAGE and I am wondering how that is computed? Thanks! Daniel ___ Freesurfer mailing list F

Re: [Freesurfer] rh or lh?

On 10/01/2013 07:45 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study

[Freesurfer] rh or lh?

Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailin

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

13 6:00 PM, "Douglas N Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

ng that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Than

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

) 737-5454 On 9/26/13 12:26 PM, "Douglas N Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Dan

[Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold..

Re: [Freesurfer] label stats?

arvard.edu>> wrote: Hi Daniel you can give it to mris_anatomical_stats with the -l command cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui "

Re: [Freesurfer] label stats?

udy Center New Haven, CT (203) 737-5454 On 9/23/13 3:40 PM, "Yang, Daniel" mailto:yung-jui.y...@yale.edu>> wrote: Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui "Daniel" Ya

[Freesurfer] label stats?

Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer m

Re: [Freesurfer] dilate a label?

ilto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Daniel, yes, mri_label2label will do this, at least the current dev version and maybe 5.3: mri_label2label | grep dilate --dilate Ndilate the label N times before writing cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Hi F

Re: [Freesurfer] dilate a label?

ri_label2label will do this, at least the current dev version and maybe 5.3: mri_label2label | grep dilate --dilate Ndilate the label N times before writing cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Tha

[Freesurfer] dilate a label?

Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] break down a label?

tom fill with "up to functional threshold" and "up to different labels" check (not sure of the exact wording). 6. Left click in a region that you want, and click fill. 7. Save the label. 8. Right click to unselect and go to 6 until you are done with all the subregions cheers Br

[Freesurfer] break down a label?

Dear FreeSurfer Experts, If I have a label that spans across multiple anatomical regions, is it possible to automatically break it down according to aparc.annot? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 __

Re: [Freesurfer] TALx coordinates

oes so nonlinearly. doug On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z =

[Freesurfer] Maximum significance

Hi all, I performed cluster analyses and obtained several clusters, which are indicated by the corresponding maximum significance levels. For example, cluster one -- 4.00, and cluster two -- 4.00. Then I did a conjunction analysis to see their overlap, and then did a mri_surfcluster to get the

Re: [Freesurfer] TALx coordinates

ut going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI30

Re: [Freesurfer] Interpretation of red/blue clusters in group analysis

you can refer to this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/12/13 9:04 AM, "Anita van Loenhoud" mailto:acvanloenh...@gmail.com>> wrote: Hi F

Re: [Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec

Just my two cents: I think the age should be mean-centered; otherwise, the meaning of the other variables need to be interpreted as age = 0 (rather than mean age = 0). In general, I believe in qdec or mri_glmfit, the effects of Class variable are interpreted as 0 on the continuous/nuisance vari

Re: [Freesurfer] TALx coordinates

if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

[Freesurfer] mri_annotation2annotation?

Hi all, I know I can use mri_label2label and then mris_anatomical_stats -l to obtain the label-based cortical thickness for each individual subject. I also know that there is a tool called mri_annotation2label. But is there a way to convert annotation to each individual subject, so that I can

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