Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions

FS permutation tutorial with the output from above (after including the --eres-save flag in the mri_glmfit command)? Kind regards, Carl On 12/12/2022 6:14 PM, Trolle, Carl wrote: > Thank you for the reply, > > 1. Once each participant's aparc has been broken and we'v

[Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions

you for your time! Kind regards, Carl Trolle Research fellow Spaulding Neuroimaging Lab Platform: linux-centos7_x86_64-7.1.1-20200723-8b40551 FreeSurfer version: 7.1.1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] Specifying contrasts for an unbalanced design

to our situation. If we do find an interaction, would that cluster then show up on the cluster summary in the glmdir-folder? Thank you and sorry for all the questions, just wanting to make sure we are doing this correctly. Kind regards, Carl Trolle Research Fellow Spaulding Neuroimaging Lab Free

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

spot (please see attached). This however seems to have caused the S_front_inf (yellow outline) to split into two. Kind regards, Carl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

(mris_register and mris_ca_label) as expert option files during recon-all to correct the incorrect parcellation of the annot.aparc-file? If so, would that also require a later Freesurfer vesion than what we’ve been using? Kind regards, Carl ___ Freesurfer

[Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

I'm sending what you asked for, otherwise I'll be happy to correct this. Kind regards, Carl terminal Description: terminal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Using averaged T1-images to calculate cortical thickness

Hi, yes that’s correct, one of the sites gets us both axial and sagittal T1s at 1mm isotropic. Ok, after some discussion I think we’ll move along without using averaged images. Thank you for taking your time! Kind regards, Carl ___ Freesurfer

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

gards, Carl From: Trolle, Carl Sent: 09 August 2022 12:37 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution Sorry, been trying to get this right for some time before getting back t

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

ate! Kind regards, Carl ___ 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

[Freesurfer] Using averaged T1-images to calculate cortical thickness

Kind regards, Carl FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Platform: CentOS Stream 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] new paper published

Hi Bruce, Would it be possible to get a reprint? I no longer have Harvard Library access. Thanks, Carl On Tue, Dec 5, 2017 at 4:46 PM, Bruce Fischl wrote: > Hi All > > we just published a paper on 3D microscopic imaging of connectivity and > architecture: > > https://www

Re: [Freesurfer] "error parsing license file, expected 4 values" with amygdala segmentation

Hi Andrew, Looks like only 3 lines. I'll see if I can locate a back up. Thanks, Carl On Wed, Nov 15, 2017 at 3:06 PM, Hoopes, Andrew wrote: > Hi Carl, > > How many lines of text exist in your license file? > > Andrew > > On Nov 9, 2017, at 8:18 AM, Carl Anderson wro

[Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0

our dataset, or is it ok with 0.57x0.57 in plane resolution and thinner slices? We are not planning on performing manual segmentation on the dataset and thus want the settings to be optimal for the Freesurfer segmentation. What about number of averages? Best regards, Carl Pintzka

[Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

n * *Using the suffix name: * * subfieldAnalysis_T1_v1.0* *And writing them to: * * test_no-T1.txt * *vermisii:RBrain carlanderson$ * Hope this helps, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<&g

Re: [Freesurfer] A few problems with freesurfer-Darwin-snowleopard-i686-dev-20150507

tvVxX ] [ argument ... ]. I thought about installing the new build but I don't see a snowleopard verson? I hope you are going to keep supporting snowleopard...any thoughts on why the recon-all you sent doesn't run with the freesurfer-Darwin-snowleopard-i686-dev-20150507 installation? Thanks!

[Freesurfer] freesurfer-Darwin-snowleopard-i686-dev.tar.gz is only 167 MB

tners site? At home I can access the site as a guest…but when I download the snowleopard build and it is only 167 MB which doesn't seem correct. Thanks for your help with this, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

Re: [Freesurfer] example in mris_label2annot's help

No...I will try running it from lables On Tue, Mar 25, 2014 at 6:04 PM, Douglas N Greve wrote: > > does it exist in the same folder that you are running the command from? > > On 03/25/2014 05:15 PM, Carl Anderson wrote: > > Oh yes, > > > > /Applications/

Re: [Freesurfer] example in mris_label2annot's help

Oh yes, /Applications/freesurfer/subjects/bert/label/aparc.annot.ctab On Tue, Mar 25, 2014 at 11:35 AM, Douglas N Greve wrote: > does that file exist? > On 03/25/2014 10:04 AM, Carl Anderson wrote: > > Dear list, > > I tried runing the example in mris_

[Freesurfer] example in mris_label2annot's help

ORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl could this be a bash vs tcsh problem as I am using bash? -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Carl Anderson souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Carl Anderson http://www.linkedin.

[Freesurfer] problem with qdec in full install of 5.2 beta

Dear Freesurfer, When trying to start qdec I get the following error: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap Any suggestions for a work around? Thanks, Carl

[Freesurfer] Problem with mri_glmfit ill-conditioned matrix

--surf fsaverage lh --cortex --glmdir ELS_CON_June26_contrast_one 2. The FSGD file (if using one) 3. And the design matrix above -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<&g

Re: [Freesurfer] correcting for normal inter-cranial variability

that what you use and whether you use it it depends again on the question you are actually asking. There are some very good and smart threads on this if you search. Mike Harms I seem to recall Carl Schwartz >>>>>>>>>>>>>>>>>>>>>>

[Freesurfer] mri_segstats for T2-relaxation time data?

25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky mailto:ni...@nmr.mgh.harvard.edu>> wrote: mri_segstats, for example: mri_segstats --se

[Freesurfer] List of midpoint talairach coordinates for each FreeSurfer cortical region?

Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

Re: [Freesurfer] mac os questions and hypo/hyper intensity question

Hi Lindsay, I have run FS on Lion (10.7.2) on a MacBook Pro with excellent results. Don't know about hypo&hyper. Carl On Wed, Nov 30, 2011 at 4:02 PM, Lindsay Ercole wrote: > Has anyone else had problems installing FS 5.1 on a Mac running OS 10.7.2? > (i.e. Lion) > > Al

[Freesurfer] ERROR running mkcontrast - in FsFastTutorialV5.1

! <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center,

[Freesurfer] Stupid FsFastTutorialV5.1/TutorialData question

) into your $SUBJECTS_DIR" My stupid question: Could this be accomplished by creating subdirectories or links in $SUBJECTS_DIR? Thanks, -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<

[Freesurfer] kvlThresholdImage fails MacOSX 10.6.8

Thanks, -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Har

[Freesurfer] GroupAnaysis Tutorial question: GLM directory error

-z.negative --sim-sign neg --overwrite With the same result. Any suggestions? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Ca

Re: [Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?

Well our primary reason for using this sequence is to better delineate the amygdala. On Wed, Feb 2, 2011 at 5:03 PM, Bruce Fischl wrote: > what do you want to do with the echoes? > > On Wed, 2 Feb 2011, Douglas N Greve wrote: > > Hi Carl, you're probably better off takin

[Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?

ectly? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroim

[Freesurfer] recon-all error

ts MNI_DIR Desktop/local/freesurfer/mni With no errors. When I give the command: echo $FREESURFER_HOME I also get back: Desktop/freesurfer Any suggestions? Thanks, Carl -- Carl Dambkowski Research Assistant Cerebral Localization Laboratory Columbia University Medical Center (212

[Freesurfer] Undefined Variable

something basic or something is completely wrong. I can access the already created files but it doesn't let me run a recon-all for some reason. Thanks for your help! Carl -- Carl Dambkowski, MS Research Assistant Cerebral Localization Laboratory Columbia University Medical Center

[Freesurfer] Antw: Re: V5/MT label anatomical borders

ce Fischl 15.06.10 14.56 Uhr >>> Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schult

[Freesurfer] V5/MT label anatomical borders

Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg

[Freesurfer] Re: Tal QA log outputs

List readers - here is a helpful clarification from Avi on my question to Nick. Thx Avi! carl -- Forwarded Message From: Avi Snyder Reply-To: Avi Snyder Date: Fri, 24 Apr 2009 01:37:50 -0400 To: , "Schwartz, Carl R.E." Cc: , Conversation: Question about Tal QC logs Subject: Re

[Freesurfer] Tal QA log outputs

? While it looks like –tal check not not automatically output the value of the atlas_transform_error term, Is the z score that DOES appear (automatically) in the log file the same z score that Avi mentions below, that compares the atlas_transform_error term to the training set? Thanks! Carl

[Freesurfer] A question about symmetry between two hemispheres

Hi Lars, In the interim you might want to take a look at thread below about this issue where I discuss some admittedly imperfect approaches pending doug's tool carl schwartz On 3/11/09 3:32 PM, "Douglas N Greve" wrote: Not yet. I have some experimental software to do this but

[Freesurfer] more inflation of average subject

below worked for us carl schwartz -- Forwarded message -- From: Bruce Fischl Date: Fri, Sep 5, 2008 at 1:26 PM Subject: Re: more inflation To: Doug Greve two things: 1. use -n , where the default is 10 (try 20) 2. -dist , where the default l is 0.1 (try something smaller

[Freesurfer] (no subject)

As far as the first, This happens sometimes when you make your own average subject. You just need to inflate it more. I will try to dig up an old email I have on the commands. As for the second, just click the redraW BUTTON CARL SCHWARTZ On 2/17/09 12:44 PM, "Devdutta W" wr

[Fwd: Re: [Freesurfer] annotation file and labels for fsaverage]

Hi Jeff - read the thread below starting with my Sept 8 2008 email. Bruce - what is the status on the insula label for aparc? carl > Hello all, > > Thank you for your quick replies to my previous posts. One more question. I am wondering what the difference is and if I should

[Freesurfer] Version 4.2.0 for Tiger on PowerPC Mac?

Hi Would it be possible to somehow download V4.2.0 for Tiger running on a PowerPC Mac? Thanks --- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Neural Imaging Center, McLean Hospital 115 Mil

[Freesurfer] A question about symmetry between two hemisphere

ing cluster, is not a biased metric. best, carl >>>>>>>>>>>> no, the vertex index is essentially arbitrary and you can't use it to compare left and right. Doug had some tools for this, but I'm not sure whether they are ready for primetime yet. cheer

[Freesurfer] comparing hemispheres

that bias would seem to be absent for the contralateral label. Carl -- Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078 On 12/2/0

Antw: Re: [Freesurfer] absolute curvature values for vertex-wise comparison

Hi Bruce, thank you very much. That' s what I looked for. Best regards, Christoph >>> Bruce Fischl <[EMAIL PROTECTED]> 13.11.08 14.43 Uhr >>> Hi Carl, you could read them into matlab, take the absolute value, and write them back out again if you want, then ru

Antw: Re: [Freesurfer] absolute curvature values for vertex-wise comparison

;>> On Thursday 13 November 2008 08:23:08 Carl Schultz wrote: > Dear all, > > for a vertex-wise comparison of the mean curvature is there a > possibility to change the signed curvature values from the preprocessed > curv.mgh to unsigned (absolute) values for the glm? > The newest

[Freesurfer] absolute curvature values for vertex-wise comparison

Dear all, for a vertex-wise comparison of the mean curvature is there a possibility to change the signed curvature values from the preprocessed curv.mgh to unsigned (absolute) values for the glm? Thanks in advance, Christoph Universitätsklinikum Jena Körperschaft des öffent

[Freesurfer] Extraction mean curvature values

Dear all, I compared the mean curvature between two groups using the mri_glmfit command and the Monte carlo simulation. Is there a possibility to extract the smoothed average curvature values of the significant clusters for all subjects? Thank you in advance Best regards Christoph Schultz Uni

Re: [Freesurfer] annotation file and labels for fsaverage

at times have more detail — though I have never asked Doug if this will always work correctly. If others have discovered pros and cons in other regions, please share. Best, Carl Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Labora

[Freesurfer] How to reorient brains collected headfirst prone

Dear Freesufers, How do I preprocess for freesurfer, heads collected headfirst prone instead of the normal headfirst supine? Thanks, Carl --- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Brain Ima