[Freesurfer] Covary for a categorical variable in mri_glmfit

!! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent

Re: [Freesurfer] Covary for a categorical variable in mri_glmfit

lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, I am trying to covary for Gender in mri_glmfit, but I

[Freesurfer] Covary for categorical variable in QDEC

Hello, Is it possible to covary for a categorical variable in QDEC? I see other posters have said it is not possible, but I did not see any official documentation or response regarding the issue. Thank You, Jeff Sadino ___ Freesurfer mailing list

Re: [Freesurfer] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab

to download the updated one at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc? We also have some people using FreeSurfer 5.1.0, mris_preproc release date 5-17-11, Revision 1.59.2.1. Do they need to update their mris_preproc script? Thank you very much, Jeff Sadino

[Freesurfer] 1 Group (2 Levels) 2 Covariates

Hello, I want to do an analysis with 1 Group (Control and HIV) with two covariates (Age and ICV). Qdec only lets me choose one covariate. So instead I choose two nuisance variables. No matter how many different permutations I run on this, I can not get it to duplicate my SAS results, and the

Re: [Freesurfer] Cortical Normalization Questions

feedback would be very greatly helpful! Mahalo, Jeff Hi Jeff, I'm confused here. ICV and surface area are two very different things. cheers, -MH On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino jsadino.que...@gmail.comwrote: Thank you everyone for your great input. After reading through all

[Freesurfer] mri_segstats memory corruption error

-bf8a1000 rwxp 00:00 0 [stack] Writing to rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat Abort Thank you for your help! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] QDEC with cluster-wise p=.1

a threshold of 1.00 (p=.1) and only the abs sign? Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person

[Freesurfer] Jacobian Questions

Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the

[Freesurfer] Cortical Normalization Questions

Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area

[Freesurfer] Exclude cortical region for one subject during qdec analysis

lobe...no pathologies, just image wraparound during acquisition :). This makes the cortical surfaces unreliable in this area. Is there a way to tell qdec to ignore the occipital regions in this one subject in its analysis? Thank you very much, Jeff Sadino

[Freesurfer] Comparing Cortical Thickness

this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino

Re: [Freesurfer] Verifying ICV in FS5

bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV.  I have a couple more questions that I am hoping you could

[Freesurfer] Verifying ICV in FS5

in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2

Re: [Freesurfer] Brain Volume measures

are based on the automatic volume segmentation. doug Jeff Sadino wrote: Hello, Thank you Bruce and Doug for your answers to my previous question about a bad talairach.lta file. I am now grabbing volumes using fs5.0.0 and would like to ask for clarification. On the Morphometry Stats page

[Freesurfer] Brain Volume measures

you for your invaluable help! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you

[Freesurfer] Fixing Talairach.lta

files are all good. Can I just copy the fs510 talairach.lta file to the fs500 subject folder, or will that cause other issues that are not obvious? As a side note, what would the tkregister2 command be to create the lta file? Thank you, Jeff Sadino

[Freesurfer] Resize window using Tcl command

Hello, I was wondering if there is a Tcl command to resize the window. I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html Thank you, Jeff Sadino

Re: [Freesurfer] Inaccurate Surfaces Generated

transforms dir using tkmedit or tkregister2. cheers Bruce On Wed, 5 Oct 2011, Jeff Sadino wrote: Hi Bruce, Thank you very much for taking a look at this for us. I uploaded it to your ftp server under the name JeffSadino_050089_S05.tar. About 70 of our subjects are showing similar problems

Re: [Freesurfer] Inaccurate Surfaces Generated

that will help, that would be great. Thank you again! Jeff On Wed, Oct 5, 2011 at 2:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi jeff Sorry, this slipped through the cracks. If you upload the dataset we will take a look Bruce On Oct 5, 2011, at 8:32 PM, Jeff Sadino jsadino.que

Re: [Freesurfer] Memory allocation problem with mri_robust_template

, but they are still freezing. Besides upgrading the entire cluster to something more current, would doubling the RAM to 8GB be worthwhile? As always, thank you so very much! Jeff Sadino Mahen Fri, 11 Feb 2011 09:16:27 -0800 To Martin, Thanks a bunch. I haven't tested out all the recommendations, but at least I

Re: [Freesurfer] Longitudinal Subject/Base name errors

You! Jeff Sadino On Wed, Aug 10, 2011 at 10:27 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: stable 5.1 contains the fix, which is the addition of -w to the grep on line 5428. that particular fix works for the example names given (11 as the basename, 11_S0 and 11_S1

[Freesurfer] Longitudinal Subject/Base name errors

. Can anyone recommend one approach over the other? Thank you very much, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

[Freesurfer] Pial Edits on Base Template

/050079 exists, delete or re-run with -force This is confusing to me because if I delete the folder, then wont my edits also be deleted? I ran it using the force flag, and it seems to be going ok. I just want to ask if this is the best way to do this. Thank you, Jeff Sadino

[Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences

will not include all possible improvements? If I want to get an accurate an ICV measurement as possible, is it advisable to rerun all of my subjects in FS5, starting from scratch? As always, thank you for your valuable assistance! Jeff Sadino ___ Freesurfer

Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences

Hello Bruce, Thank you for your reply. I used recon-all -make all -s subject. Thanks, Jeff On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jeff what command did you run to run them over? cheers Bruce On Thu, 16 Jun 2011, Jeff Sadino wrote: Hello

[Freesurfer] ICV smaller than the brain

for this be, and are there any other tricks that I could use? Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] Visualizing Subcortical Volume Differences

direction? Thank you, Jeff Sadino On Mon, Apr 11, 2011 at 1:07 PM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls

[Freesurfer] Visualizing Subcortical Volume Differences

Thalamus and the Study Thalamus. I have seen a couple of different ways to do this, but they all seem rather clunky. Can anyone recommend a method for this? Thank you very much, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Resampling Question

be of pushing data through the FreeSurfer reconstruction pipeline that is not really 1x1x1 isovolumetric? Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Resampling Question

One more thing that might be useful: for my current dataset, everything was processed in FreeSurfer 4.3.1. Thank you, Jeff On Mon, Mar 7, 2011 at 12:41 PM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, I have a question about the effects of FreeSurfer's resampling algorithms. The way

[Freesurfer] recon-all -make all error?

, but there is no label/?h.BA*.label or label/?h.entorhinal_exvivo.label files. Looking at the recon table, it looks like these are supposed to be part of the standard recon. Is my -make all broken, or can I ignore this message? Thank you, Jeff Sadino ___ Freesurfer mailing

[Freesurfer] BrainSegVol different in wmparc and aseg

not fix it, should I take the BrainSegVol from the aseg.stats file? Thank you! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

[Freesurfer] fs450 Longitudinal edits, varied data, and other questions

step? My feeling would be no, that I could only do that if the subject does not move, but I wanted to check. Sorry for the long questions! Thank you for all of your great help all the time! Jeff Sadino ___ Freesurfer mailing list Freesurfer

[Freesurfer] Surface Area and Cortical Volume

Hello, As I understand it, the surface area measure is not a real surface area measure. It is more a measure of how much the brain has to be stretched in order to get into a common space. My question is that if the cortical volume is calculated by multiplying the thickness and the surface area

[Freesurfer] make_average_surface error?

, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1. Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] 3-Way Anova in Qdec

discrete factor in the qdec design tab, it deselects one of the others. Does it max out at two? Thank you very much, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Mixing fs 4.3.1 with fs 4.5.0 longitudinally

4.3.1 subjects into the 4.5.0 longitudinal stream, or will I have have to redo the cross-sectional reconstruction in 4.5.0? Thank you very much, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Calc stats on ROI in qdec

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole

[Freesurfer] Calc stats on ROI in qdec

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole

[Freesurfer] qdec Font Error

all of the windows fonts on my Linux. Haven't looked at OpenGL yet. Am I just missing the right font, or is there a deeper problem? btw, Freesurfer 4.3.1 is installed on a server that I log into. Thank you again! Jeff Sadino ___ Freesurfer mailing list

Re: [Freesurfer] ICV Error fs 4.3.1

copy talairach.auto.xfm to talairach.xfm. n. On Fri, 2010-02-19 at 17:41 -0500, Douglas N Greve wrote: Can you check the talairach.xfm and the talairach_with_skull.lta to make sure that they are different across subject? Jeff Sadino wrote: Hi Doug, Thanks for the quick reply

Re: [Freesurfer] ICV Error fs 4.3.1

of the values are similar except the icv. Do you guys have any ideas where I can look for the answer? Thank you very much, Jeff On Thu, Feb 25, 2010 at 11:14 AM, Jeff Sadino jsadino.que...@gmail.comwrote: Doug - Thank you for your suggestion. I looked, and the talairach_with_skull.lta file

[Freesurfer] ICV Error fs 4.3.1

2009/02/11 22:38:51 nicks Exp $ Thanks! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ICV Error fs 4.3.1

of these subjects in fs3 a while ago using an older version of my script, and they all came out with unique icv values. Thank you again for your suggestions! Jeff Sadino On Fri, Feb 19, 2010 at 12:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The ICV is *estimated* from the talairach

[Freesurfer] Measuring Cortical Volume

. I am still looking at the pallidum differences and will let you know soon. Thanks! Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Smaller

, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Co-vary

Hello Freesurfers, My apologies for this very basic question more about statistics than freesurfer, but I have not found an answer anywhere on the wikis, or the web (maybe it is too basic :-) ) I am interested in age-related effects of hiv and I wanted to covary for age and education in

[Freesurfer] mri_glmfit significiance verification outside freesurfer

? Thank you very much, Jeff Sadino _ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_SD_25GB_062009___ Freesurfer mailing list

RE: [Freesurfer] mri_glmfit significiance verification outside freesurfer

stores the -log10(p), not p, so to get the true p-value of say, -2 (in the sig.mgh), take 10^-2 (giving you the true p-value of 0.01). Nick On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote: Hello Surfers, I am trying to verify the p-value sig.mgh maps outputted from

[Freesurfer] mris_preproc really averages?

Hello, I think my message got scrubbed from my last post with the pictures. I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two

[Freesurfer] Extracting Thickness Vertex Values

. Otherwise, I'll use the mris_convert command on each subject to make an ascii file. As always, thanks for your expert help! Jeff Sadino _ Windows Live™: Life without walls. http://windowslive.com/explore?ocid

[Freesurfer] New Tutorial Attachments

are not allowed to attach a file to this page. I see the page was recently updated for the new class. Are the powerpoints still available to view somewhere? Mahalo, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels

[Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1

will cause differences in the analysis. As I read on a previous post, freesurfer resamples all its input data into 1mm isovolumetric voxels anyways, so I should be ok? Regards, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news

RE: [Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing from 1.4x1.4x1.4 mm slices to 1x1x1 Hi Jeff, are you intending to combine them into a single study? This can be problematic as you'll get differential sensitivity and possibly bias. cheers, Bruce On Tue, 17 Mar 2009, Jeff Sadino wrote

[Freesurfer] tksurfer Load Group Descriptor File error

/share/apps/freesurfer/subjects SynthSeed1237057379 In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http

[Freesurfer] Are accurate volumes necessary for accurate surfaces?

Hello Surfers, I want to do a study on the cortical thickness for some new subjects. As I understand the Recon process, the surface files get their information from the volume files. If I want to increase the accuracy of my thickness files, do I first need to manually check the accuracy of

[Freesurfer] Configure Overlay Display for 2 Colors

with the min, max, mid, and piecewise options every way I can think of. Is there some way to get a fuller color spectrum on my overlay? Thank you, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http

RE: [Freesurfer] Configure Overlay Display for 2 Colors

the picture much more descriptive to look at. Thanks for your help! Regards, Jeff Sadino Date: Mon, 2 Mar 2009 17:28:08 -0500 From: fis...@nmr.mgh.harvard.edu To: jsad...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Configure Overlay Display for 2 Colors Hi Jeff

[Freesurfer] GLM Contrast

ed, cd ed, nc ed Will this matrix file work for my hypothesis? It seems like if the last 6 are zeros, then it will not be taking age and education into account? And then also, since I have 90 subjects in all, will I need to correct for multiple comparisons? Thank you in advance, Jeff Sadino

[Freesurfer] Group Cortical Thickness

the processing could be done fairly quickly. Thank you in advance for your advice! Jeff Sadino _ Stay up to date on your PC, the Web, and your mobile phone with Windows Live. http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct

FW: [Freesurfer] Group Cortical Thickness

, Jeff Sadino Date: Wed, 18 Feb 2009 19:25:21 -0500 From: gr...@nmr.mgh.harvard.edu To: jsad...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Cortical Thickness If this is just a thickness study, then you dont need fsfast. There are examples/tutorials

[Freesurfer] lh.aparc.a2005s.stats and lh.aparc.stats differences

is that lh.aparc.a2005s.stats was made with ?h.atlas2005_simple.gcs and lh.aparc.stats was made with ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs. Which one is more accurate? I am using freesurfer 3.0.5. Thank you, Jeff Sadino

[Freesurfer] Measuring regional cortical thickness

the surface in tksurfer in a similar way that you can in tkmedit? Thank you very much. Jeff Sadino _ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid

[Freesurfer] Calculate corticol thickness

/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /share/apps/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl (And then File - Load Curvature - lh.thickness) % surfer: curvature read: min=0.226951 max=5.00 Thanks you very much, Jeff Sadino

[Freesurfer] Count non-zero voxels without matlab

Hello surfers, I would like to count the number of non-zero voxels in the image brain.mgz. Does anybody have any ideas what the easiest way to do this would be without using matlab? Thank you all! Jeff Sadino _ Want to do more