Re: [Freesurfer] number of vertices

eesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: >it's 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 vertice

[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:

Re: [Freesurfer] number of vertices

gt;of the white matter for each hemisphere. > >cheers >Bruce > > >On Mon, 29 Feb 2016, Yang, Daniel wrote: > >> Dear FreeSurfer experts, >> >> Can you please indicate the number of vertices FreeSurfer use in each >>hemisphere to reconstruct the brain

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" <daniel.yj.y...@yale.edu>

Re: [Freesurfer] mri_convert and image orientation

ecessarily. For FSL, the determinant must be less than 0 (see >mri_info output). Having said 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

Re: [Freesurfer] mri_convert and image orientation

eesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >If the determinant is less than 0, then it is radiological (probably it >will be radiological). > >On 01/26/2016 04:20 PM, Y

[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

Re: [Freesurfer] TalX TalY TalZ

gh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TalX TalY TalZ If you use --fixmni, then they are reported in approximate talairach space On 11/11/15 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, Are these coordinates reported in mri_surfcluster

[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

Re: [Freesurfer] mri_surfcluster statistics and label question

Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> 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, >>

[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

Re: [Freesurfer] convert label to mgh

eesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >use mri_label2label 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?

Re: [Freesurfer] mri_surfcluster statistics and label question

rd.edu> wrote: > > >On 11/09/2015 10:51 AM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> In the output mri_surfcluster (e.g., >> >>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisCluster >>Summary), >> what is the statis

Re: [Freesurfer] Curvilinear interaction with age

> wrote: >Hi Daniel, > >you can always specify your own design matrix X in 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

[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

[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

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: > on behalf of Daniel Yang

[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] 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

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

n always convert to nifti via: > >mri_convert cluster.mgh cluster.nii > >and 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.mg

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

cheers Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three

[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

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

2015, Yang, Daniel wrote: 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

Re: [Freesurfer] visualize subcortical areas in tksurfer?

. For 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 in a figure. Sometimes we do see some subcortical activation (like

Re: [Freesurfer] visualize subcortical areas in tksurfer?

a 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 what you

[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

Re: [Freesurfer] extract individual label from Destrieux Atlas

@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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

[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

Re: [Freesurfer] visualize subcortical areas in tksurfer?

Daniel 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: Dear FreeSurfer experts, I find

[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

Re: [Freesurfer] mri_label2label results

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 CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer

Re: [Freesurfer] mri_label2label results

? Is the difference between 1 and 3 trivial? Thanks! Daniel On 6/19/14, 8:13 PM, Yang, Daniel yung-jui.y...@yale.edumailto: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 6/19

Re: [Freesurfer] mri_label2label results

it was a bug 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

Re: [Freesurfer] mri_label2label results

On Jun 19, 2014, at 10:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto: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 yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks! Is there a list of bug fixed

Re: [Freesurfer] subcortical segment NIFTI files

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 the input

Re: [Freesurfer] subcortical segment NIFTI files

On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. Best, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer

Re: [Freesurfer] subcortical segment NIFTI files

segment NIFTI files They look pretty similar. 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

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 gr...@nmr.mgh.harvard.edumailto: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

Re: [Freesurfer] subcortical segment NIFTI files

was trying to find out what it is you 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

Re: [Freesurfer] subcortical segment NIFTI files

registration. Use $FREESURFER_HOME/average/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

Re: [Freesurfer] subcortical segment NIFTI files

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 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

[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

Re: [Freesurfer] subcortical segment NIFTI files

, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: 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

Re: [Freesurfer] subcortical segment NIFTI files

neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edu 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 files in MNI152 space as NIfTI files, for example, the different

[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

[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

Re: [Freesurfer] Frontal WM volume

and 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 FreeSurfer? Much obliged, Daniel

[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] MeanThickness

automatically 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

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 yung-jui.y...@yale.edumailto: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

12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto: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

Re: [Freesurfer] WM vol as measure

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 New

Re: [Freesurfer] WM vol as measure

wrote: It should be there if the recon did not fail. The file is called 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

Re: [Freesurfer] WM vol as measure

, Yang, Daniel wrote: Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New

[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] WM vol as measure

:18 PM, Yang, Daniel yung-jui.y...@yale.edumailto: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 regions

[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

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 filled

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

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-step example

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

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 the helps! I also find

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

...@nmr.mgh.harvard.edu 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: Thanks for both of you

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

...@nmr.mgh.harvard.edumailto: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, what command

[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,

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

to 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

[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 Study

[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

[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] 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, Yang

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

...@nmr.mgh.harvard.edumailto: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, I am

[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

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 not described in http

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 gr...@nmr.mgh.harvard.edumailto: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

[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

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

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. Error

[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

[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

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 Center New Haven, CT (203) 737-5454

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

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 yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps

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

N Greve gr...@nmr.mgh.harvard.edumailto: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 checking

[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 mailing

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

On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto: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, Daniel wrote

[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

Re: [Freesurfer] label stats?

New Haven, CT (203) 737-5454 On 9/23/13 3:40 PM, Yang, Daniel yung-jui.y...@yale.edumailto: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 Yang, PhD Postdoctoral

[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

Re: [Freesurfer] label stats?

wrote: Hi Daniel you can give it to mris_anatomical_stats with the -l label 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 Daniel Yang, PhD

[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] break down a label?

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 Bruce On Sun, 22 Sep 2013, Yang, Daniel

[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

Re: [Freesurfer] dilate a label?

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? Thanks! Daniel

Re: [Freesurfer] dilate a label?

It seems that only in dev version, mri_label2label supports dilation. But I find that in 5.3, mris_label_calc is able to perform dilation too! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/22/13 9:38 PM, Yang, Daniel

Re: [Freesurfer] TALx coordinates

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 = (-0.0130) MNI305

Re: [Freesurfer] TALx coordinates

without 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) MNI305x

[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

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

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

[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

Re: [Freesurfer] TALx coordinates

? 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? Best, Daniel -- Yung-Jui Daniel

Re: [Freesurfer] convert .mgh to .label?

(203) 737-5454 On 9/9/13 6:40 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: You cannot. You will have to do the conjunction on the cluster sig files, then extract a label from that. On 09/09/2013 06:30 PM, Yang, Daniel wrote: Thanks so much! I used

[Freesurfer] TALx coordinates

Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the

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