RE: [Freesurfer] mri_glmfit significiance verification outside freesurfer

Those differences are much too large to be rounding errors. Are you sure that you are running identical models in mris_glmfit and SAS, and that the data that you are testing in SAS is in fact what is being processed in mris_glmfit (e.g., same degree of smoothing)? -Mike H. > > Hello Everyone, >

Re: [Freesurfer] total gray and white matter volumes, and total brain volume

Dana, Here's an approach that I use for total brain volume (without the cerebellum): Compute the total volume enclosed within the pial surface (mris_volume lh.pial) and then subtract out the volume from the aseg.stats for the Lateral-Ventricle and choroid-plexus). Repeat for both hemispheres, a

Re: [Freesurfer] Details about aseg Stats

If you visualize the segmentation (aseg.mgz) in tkmedit you can see exactly what is labeled Cerebral-White-Matter and Cerebral-Cortex based on the volume (not the surface) segmentation. As for the "Intracranial Volume" value in the preamble of the aseg.stats file, that is a statistical estimate o

Re: [Freesurfer] mri_surf2surf

Hi Jidan, The surface in the native space is given by ?h.white. ?h.sphere and ?h.sphere.reg provide the "mapping" of those vertices of to a spherical representation, and registered spherical representation, respectively. There are ways to get at the Jacobian of these transformations if that is w

Re: [Freesurfer] freesurfer's template for sphere registration

Hi Jidan, It sounds to me that what you're asking is whether it is possible to invert the "mapping" from {lh,rh}.white to {lh,rh}.sphere, but apply that inversion to {lh,rh}.sphere.reg, thus generating a putative "{lh,rh}.white.reg" surface. I'm not sure that operation is possible, or if the resu

Re: [Freesurfer] contrast matrix question

Hi Tori, There is no way to investigate the interaction of two continuous effects with the contrast vector alone, if the design matrix itself only involves main effect terms. The interaction itself needs to be coded into the design matrix. Note that it can become tricky as to the proper coeffici

Re: [Freesurfer] contrast matrix question

be set up to handle that (as noted by Doug). If by interaction you mean the product of two continuous main effects, then that needs to be coded into the design matrix, and the caveats that I mentioned become applicable. cheers, Mike H. On Wed, 2009-08-05 at 15:10 -0500, Michael Harms wrote: >

Re: [Freesurfer] modifying dicom headers

You might want to check out the "DicomBrowser" as well, which can change many files at a time (e.g., for an individual subject), although I don't know if it can be made scriptable. http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp cheers, Mike H. On Wed, 2009-08-05 at 15:31 -0400, Chris Wats

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for "modern" MPRAGE

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > On Aug 26, 2009, at 8:41 AM, Bruce Fischl

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

the same as > that now used by Siemens. > > Nick > > On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: > > No, our current "CAP" MPRAGE at WU on the 3T TimTrio is very similar to > > the "ADNI" mprage, so that old flag shouldn't be used

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

which it is we have to try to figure out the contrast and noise > characteristics (spgr has worse contrast and less noise) > > On > Wed, 26 Aug 2009, Michael Harms wrote: > > > > > Ok, now I'm confused again, because my understanding is that the Andre > > v

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

gr and mprage (or neither, > depending on your perspective). You're probably right that mp-rage is more > common these days, but I think spgrs are still fairly widespread on GE. > > On Thu, 27 Aug 2009, Michael Harms wrote: > > > > > So, are you saying that the

Re: [Freesurfer] FDR correction

Your FDR analysis sounds correct. You probably have a rather small number of "marginally" significant vertices, which is why none survive FDR. You could try increasing the "q" value from say 0.05 to 0.1, in which case 10% of the surviving vertices would be expected to be false positives. cheers

Re: [Freesurfer] FDR correction

tp://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html > > On 10/16/2009 09:58 AM, Michael Harms wrote: > > Your FDR analysis sounds correct. You probably have a rather small > > number of "marginally" significant vertices, which is why none survive &

Re: [Freesurfer] TIV corrected

No. They are the volumes in the subject's native space. -MH > > Hi, there, > > Have those volume of ROIs in aseg.stats been TIV corrected? > > > > > Thanks a lot! > > Guang > > _ > Hotmail: Free, trusted and rich email service. > h

Re: [Freesurfer] About corrected t-statistics and p-values

Hello Jorge, There is no such thing as a "corrected p-value" for a FDR analysis. FDR returns a p-value threshold (for the original vertex or voxel-wise p-values) such that if you threshold the data at that p-value, you can expect on average that the fraction of false-positive vertices will be equa

Re: [Freesurfer] comparison of mean thickness of gyri in two groups

To me, it makes much more sense to use mean cortical thickness as a covariate for thickness-based analyses. cheers, Mike H. > Hi Mehul, > > the MNI group had an abstract showing that thickness didn't need eTIV > correction at HBM a number of years ago, and it has been our experience > as well. >

Re: [Freesurfer] comparison of mean thickness of gyri in two groups

rus measurement (pre-central gyrus in this example) with > the mean cortical thickness. However, in most of the papers I have > only seen age and gender used as co-variates. > > > Thanks > Mehul > > > > On Sun, Nov 1, 2009 at 4:44 PM, Michael Harms > wrote:

Re: [Freesurfer] ICV/brain volume

Here is an approach that will be easier, and involves less back and forth between the surface and volume-based streams (and thus should be more accurate): Just use 'mris_volume' to get the volume of everything enclosed by the pial surface, which if I recall correctly will include the lateral vent

Re: [Freesurfer] ICV/brain volume

edit subjid T1.mgz lh.pial > -aux-surface rh.pial): part of two important brain structures, amygdala > and > hippocampus, is not enclosed in the pial surface. Is there a way to > resolve > this issue? > > Thanks, > Xiangchuan > > -Original Message- >

Re: [Freesurfer] ICV/brain volume

tats. > > Thanks, > Xiangchuan > > >> -Original Message- >> From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] >> Sent: Saturday, January 09, 2010 13:34 >> To: Bruce Fischl >> Cc: Michael Harms; Xiangchuan Chen; freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_diff geometry differences

Hello, What do "geometry differences" represent in the output of mri_diff? i.e., What do the numbers in the following output from mri_diff represent? Volumes differ in geometry 1 4 0.15 Volumes differ in geometry 2 1 0.00 thanks, -Mike H. -- Michael H

[Freesurfer] user specified output orientation using mri_convert?

the message: in nii format, but I got the message: reordering axes... MRIreorder: incorrect dst width error reordering axes I've checked the archives, and read through the mri_convert help, but just can't seem to figure out if reordering from one orientation to another (without resampling

Re: [Freesurfer] user specified output orientation using mri_convert?

be able to do it with --reorder4 (and not > --reorder) in combination with --out_orientation. --out_orientation > should not resample. > > doug > > Michael Harms wrote: > > Hello Doug, > > Is it possible using mri_convert to just reorder the way in which the > > d

Re: [Freesurfer] user specified output orientation using mri_convert?

, -MH On Fri, 2010-02-05 at 14:30 -0500, Douglas N Greve wrote: > > Michael Harms wrote: > > Hi Doug, > > > > Is --reorder4 a new feature in one of the more recent releases? > > (Currently, I'm using mri_convert from v4.1.0, and I don't see a -- > &

Re: [Freesurfer] Covariates in qdec

And for the comparison to be appropriate, you further have to make sure that you are using the exact same main and interaction terms in SPSS as are being used in QDEC. The mere presence of interaction terms in a model can have big effects on the significance (or lack thereof) of the main effects.

Re: [Freesurfer] Covariate for results of cortical parcellation

Hi Joost, If you want to control for possible global differences in thickness, then an appropriate covariate of some sort is need. To me, a logical covariate for a thickness analysis is the mean cortical thickness, as this is more directly related to the measure of interest than something like th

Re: [Freesurfer] Question about cortical surface area

Hi Massieh, There were some posts related to this a while back. If I recall correctly, the vertex-wise area measure (and likewise the vertex-wise volume measure) is highly dependent on the local mesh triangulation, and thus is not really a meaningful variable from a biological perspective. So, yo

Re: [Freesurfer] Group comparison

The data in aparc.stats contain surface area, gray matter volume, and average thickness for whole regions, and are not intended for surface display. If you want to analyze those regional values use 'aparcstats2table' and then import the data into your preferred statistical package for further ana

[Freesurfer] calculation of total cortical gray matter volume

Hello FS-list, Could you please confirm the recommended current approach for calculating the total cortical gray matter volume. Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculatio

Re: [Freesurfer] mris_anatomical_stats

Hello List, Just to clarify: I thought that the "total white matter volume" statistic that is output as part of 'mris_anatomical_stats' is incorrect and not to be used. Rather, I thought 'mris_wm_volume' was to be used instead... Also, while I'm posting on this issue, could someone please comm

[Freesurfer] nature of mris_anatomical_stats problem in v3.0.5

Hello, The FS release notes for v3.0.5 state: "mris_anatomical_stats produces incorrect results. There is no work- around. A replacement for Linux is here. This fix will appear in the next release." Is the entire output of 'mris_anatomical_stats' incorrect, or just one part of it? And, does the

Re: [Freesurfer] nature of mris_anatomical_stats problem in v3.0.5

tomical_stats, as called by > recon-all, are correct for all distributed versions of Freesurfer. > > It is only if the argument is used, and a surface other > than pial is specified, that the bug exposes itself. > > Sorry for the misinformation. > > Nick > > &

[Freesurfer] Next Release

Hello, There have been several mentions on this list of the intent to release a new FS version later this summer. As an aid to those trying to decide whether it is worthwhile to wait for the next version to start an analysis of a new group of subjects, I thought it would be helpful to know the fo

[Freesurfer] mris_anatomical_stats: differences in output between -a and -l flags

s that are output for that structure do not match those in lh.aparc.stats except for average thickness. Is a difference to be expected between the -a and -l approaches for obtaining statistics via mris_anatomical_stats? What is the source of this discrepancy? thanks, Mike H. -- Michael H

Re: [Freesurfer] Doubt in thickness computation

Hi Jorge, I'll take a stab at this since it sounds like many of the FS developers are out of town currently, but I'm just an FS user, so hopefully an FS developer can confirm whether my response is accurate. Each vertex on the pial surface has a one-to-one correspondence with another vertex on th

[Freesurfer] ordered list of boundary coordinates

Hello, Is there a convenient way using the FS tools/utilities to generate the X,Y,Z coordinates of the path of the boundary of a specified parcellation region on pial surface? thanks, Mike H. -- Michael Harms, Ph.D. Conte

[Freesurfer] loading surface as a weighted graph

f the existing FS/Matlab 'read' functions that are already available). But, if anyone already has existing code that they are willing to share, I'd appreciate hearing from you. cheers, Mike H. -- Michael Harms, Ph.D.

[Freesurfer] previous FS versions

Hello, Is it possible to get a version of Freesurfer other than the most current? In particular, I'm interested in getting a copy of v3.0.5 for the CentOS (RHEL 4) Linux platform. thanks, Mike H. -- Michael Harms,

[Freesurfer] midline parcellation bug fix

as "During cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), are mislabelled as corpus callosum or "unlabelled subcortical". A fix for this is in the works, possibly for the next release." t

Re: [Freesurfer] midline parcellation bug fix

fix for what was described in the "Known Issues" of v3.0.5 > > as "During cortical parcellation, areas of the anterior cingulate cortex > > (rostral anterior cingulate in the parcellation atlas), are mislabelled > > as corpus callosum or "unlabelled subcortical"

Re: [Freesurfer] midline parcellation bug fix

ix that affects the > >> volume > >> > segmentation (aseg) or the surface parcellation (aparc)? > >> > > >> > Is that the fix for what was described in the "Known Issues" of v3.0.5 > >> > as "During cortical parcellation, areas of

[Freesurfer] how/where is talairach.xfm used?

1 under v4 but then switch to v3 for autorecon2 & 3 so as to maintain compatibility with other subjects processed under v3? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washingt

Re: [Freesurfer] how/where is talairach.xfm used?

vi!). > > Bruce > > On Thu, 11 Oct > 2007, Doug Greve wrote: > > > It is not that important from a recon standpoint. However, if you intend to > > report talairach coods, create an average surface, or use that talairach > > transform in any way, it

Re: [Freesurfer] how/where is talairach.xfm used?

report talairach coods, create an average surface, or use that > talairach transform in any way, it will be a problem. > > doug > > Michael Harms wrote: > > >Hello, > >We are running FS v3.0.5 on some elderly brains, and the talairach > >transform (as assessed via tkr

[Freesurfer] hyperthreading

rage) just twice as long? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615

[Freesurfer] mgz header dump

I'm sure this is trivial, but I can't find the answer: How do you dump the header contents of an mgz file to the terminal? How about the optional information stored after the image data? thanks, Mike H. -- Michael H

[Freesurfer] talairach failure detection

d=0.0050) #-- Is this something that anyone else has noticed so far? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Depar

[Freesurfer] ReconAllDevTable

ate for previous stable releases? If so, it would be great if the wiki contained links to those. If not, it might be helpful to create such "snapshots" of the ReconAll flow table so that there is a convenient place to access the process flow that is most accurate for previous (non-develop

[Freesurfer] tkregister2: target vs. movable designation

equired mov and targ specifications with using the --xfm flag directly... thanks for clarifying, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Depar

Re: [Freesurfer] eTIV Normalization Issues

Hi Jason, Interesting to compare the two approaches -- I've thought some about the issues involved in the past, so I'll add my $0.02 in the hope it might benefits others on the list as well. One conceptual potential note of caution: Because the aparc stats and aseg stats are two very different pr

[Freesurfer] mris_smooth and 'NoRandomness'

d values, the output is identical. thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Roo

[Freesurfer] reading DICOM fields

t can do this, but I've tried without success to locate a Linux executable that could do the same. Does anyone out there know of one? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental

[Freesurfer] -noaparc flag

Hello, What is the role of the -noaparc flag in 'mris_make_surfaces' of FS v4? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

Re: [Freesurfer] -noaparc flag

ote: > Hi Mike, > > if noaparc is not given, mris_make_surfaces will look for ?h.aparc.annot > and read it in to determine what regions it should disable the deformation > in to avoid crossing the midline. > > cheers, > Bruce > > > On Fri, 14 Dec 2007, >

Re: [Freesurfer] left and right wm neighbors error

Hello, Just a brief addendum: Our previous experience with -autorecon2 has been primarily with v3.0.5 (and thus v3.0.5 asegs, not 4.0.1 asegs as Matt initially indicated) where we have never encountered this "nbrs" error during mri_fill. We have just started processing some new brains through -au

[Freesurfer] Qdec with v3

can't be used on v3 processed data? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital,

[Freesurfer] jacobian analyses

it just D that is set to zero)? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615

Re: [Freesurfer] jacobian analyses

inite or very > close to singular areas) > > cheers, > Bruce > > > On Fri, 21 Dec 2007, Michael Harms wrote: > > > > > Hello, > > I'm going back and running the jacobian analyses (using v4 recon-all) so > > that I can look at distortion ar

[Freesurfer] Aseg stats and white surfaces

ce Aseg Stats is not automatically rerun as part of those flags. Perhaps "set DoSegStats = 1" should be included as part of any flag that results in new ?h.white surfaces? cheers, Mike H . -- Michael Harms, Ph.D. Conte

[Freesurfer] qdec error

elated, but this had no effect. thanks for any insight, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Ho

[Freesurfer] focus in tkmedit

at a location other than where the mouse cursor was located when the left-click was performed. Consequently, I have a hard time getting the "Multiple Orientations" view to display as I want. Is there a way around these behaviors? t

[Freesurfer] losing aseg edits

there an easy way to get the CC segmentation while still preserving any previous aseg edits? cheers, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medic

[Freesurfer] clarification on computation of stats for "unknown" label in aparc

ces that are considered to correspond to cortical gray matter, based on the aseg.mgz?) thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine D

[Freesurfer] checking accuracy of talairach_with_skull.lta transform

the accuracy of the talairach_with_skull.lta transform. In your experience, is the the talairach_with_skull.lta transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate version dependent?) thanks, Mike H. -- Michael Harms, Ph.D. --

[Freesurfer] checking accuracy of talairach_with_skull.lta transform

m the determinant of "talairach_with_skull.lta". So, if we want to use the eTIV values as a covariate, should we be verifying the accuracy of this transform? And if so, what would the syntax be to do this in tkregister2 ? thanks, Mik

[Freesurfer] autorecon1 errors

is some possibility of a bad talairach_with_skull registration (6 of 80 in this particular subject set). thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School

Re: [Freesurfer] QDEC limited regressors

While on the topic of future qdec versions: Is there any plan to develop a qdec that would support simultaneous analysis of the left and right hemisphere in a repeated measure type framework? (e.g., so that you could easily create statistical maps of the main effect of group, the main effect of h

[Freesurfer] loading previous qdec analysis

Hello, Having previously saved a qdec-based analysis (i.e., "Design Name"), is it possible to reload/review that analysis within qdec? (Is "Load Project File" involved somehow?) thanks, Mike H. -- Michael Harms, Ph.D. --

[Freesurfer] purpose of creating own "average subject"

nderstand what I'm missing here. thanks, Mike H. P.S. Am I correct in presuming that the same 40 subjects were used for the Desikan GCS atlas and for deriving the spherical registration (.tif) target? -- Michael Harms, Ph.D. -

Re: [Freesurfer] purpose of creating own "average subject"

ly different from the ones in our atlas (e.g. young kids maybe). > > cheers, > Bruce > > > On Thu, 27 Mar 2008, Michael Harms wrote: > > > > > Hello, > > There have been numerous posts recently related to the creation of a > > study specific "average

Re: [Freesurfer] purpose of creating own "average subject"

there probably isn't much difference, but > there's really no reason *not* to visualize on the average anatomy of your > subjects, except to make cross-study comparisons easier. > > cheers, > Bruce > > > On Thu, 27 Mar 2008, Michael Harms wrote: >

[Freesurfer] converting a region defined by a surface to a label file

of vertices as well. thanks for your suggestions, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard

[Freesurfer] SurfaceRAS space

quot;ras" center of the volume will shift by 1 voxel in physical space when you reverse the orientation of a given axis (given the use of a 0-based volume indexing scheme). Correct? Hope my questions are clear. I know that these various transformations can be tricky to get just right. t

[Freesurfer] --label2path option in mri_path2label

my question is whether the "--label2path" option is supported, and if so, how is it intended to be used? (The output message implies that the path already has to be "encoded" somehow in the label file itself?) thanks, Mike H. -- Michael Harms, Ph.D. -

[Freesurfer] --label2path option in mri_path2label

Hi all, Can anyone comment on the --label2path option of 'mri_path2label' and how it is supposed to be used? (Or is that Doug's domain?) thanks, Mike H. - Hello, I'm trying to get the vertices of the border/edge/boundary (whatever you want to call it) of a contiguous, close

Re: [Freesurfer] LGI of annotated cortex

Just a thought, but I suspect that the volume is calculated as some product of area * "thickness". Then, with the -t option, what FS is using as thickness is now really the lgi value. So, the "volume" value is really not appropriate in that case. cheers, Mike H. On Fri, 2008-05-09 at 15:28 +

Re: [Freesurfer] Combining two regions

Hello, I also need to compute a weighted average thickness across some of the labels, so I went ahead and tested how FS empirically handles this issue. Let me say first off that Doug's recommendation of weighting by the surface area (rather than number of vertices) is imminently reasonable and in

Re: [Freesurfer] Topological defects in LGI

Hello, Here is a related question prompted by this thread, perhaps based on a misconception on my part: I was under the impression that you are guaranteed to get surfaces with an euler number of 2 under the "new" topology fixer of version 4 (which runs by default if the "old" fixer does not initi

Re: [Freesurfer] Topological defects in LGI

ituation Martin? thanks, Mike H. On Mon, 2008-06-09 at 15:03 -0400, Bruce Fischl wrote: > Hi Mike, > > I think it is the case. Sorry, I haven't been following this thread. Do > you find situations in which the corrected surfaces have the wrong > topology? > > Bruce

Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5

Hi Paul, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Incidentally, using the -eTIV option of mri_label_volume, you can also specify other transforms (e.g.

[Freesurfer] change in default GCA file

ases (4.0.3 or later)? Is the difference in the GCA minor enough that it would be reasonable to intermix data processed under 4.0.5 and 4.0.2, without needing to update the v4.0.2 data? e.g., Does the difference have any relevant impact on the subcortical segmentation? thanks, Mik

Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats

Hi Chris, Doug, please correct me if I'm wrong, but the original gm/wm segmentation contained in aseg.mgz is based on the 3D volume-based tissue segmentation. This original segmentation then forms the basis for all subsequent additional segmentations of either GM or WM in the 3D volume. That is,

Re: [Freesurfer] Watershed Error

Did you explicitly check the quality of talairach_with_skull.lta? Also, what version of FS are you using? We previously had encountered that error in 5 brains processed under FS 4.0.2, and all five of those had errant talairach_with_skull.lta transforms. Generation of talairach_with_skull.lta wa

Re: [Freesurfer] What is included in the ICV value

Now I've become confused. ICV is based on the determinant of talaiarach_with_skull.lta, for which the skull is not stripped. So, I've always assumed that basically everything -- wm, gm, csf, cerebellum, dura, AND skull tissue -- all "contribute" to the definition of the transform (using whatever

Re: [Freesurfer] What is included in the ICV value

again (or ask > Randy :>) > > Bruce > > On Thu, 4 Sep > 2008, Michael Harms wrote: > > > > > Now I've become confused. > > > > ICV is based on the determinant of talaiarach_with_skull.lta, for which > > the skull is not stripped. So,

Re: [Freesurfer] dicom image viewer

mricro is a handy viewer for instances where you've already used another tool to create an explicit volume (e.g., Analyze, nifti format, etc). For instances where you have a bunch of unorganized DICOMs, you may be interested in trying out the DicomBrowser available from the Neuroinformatics Gro

Re: [Freesurfer] GM and thickness

Hi Kelly, See also these threads where I advocate using mean cortical thickness as an appropriate covariate for a thickness analysis: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11987.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13459.html Mean cortical th

[Freesurfer] [Fwd: Re: Different slices number for control group]

Sorry, my initial reply went to just to Laura, and not the list. -MH Forwarded Message From: Laura Verga To: Michael Harms Subject: Re: [Freesurfer] Different slices number for control group Date: Tue, 8 Jun 2010 17:13:14 +0200 Hi MIchael, thanks so much for your answer

Re: [Freesurfer] Grey Matter Density?

I'll help Bruce out here :) See Panizzon et al, Cerebral Cortex, 2009, 19:2728-35 http://www.ncbi.nlm.nih.gov/pubmed/19299253 and Winkler et al, Neuroimage, 2009 (in press) http://www.ncbi.nlm.nih.gov/pubmed/20006715 cheers, -MH On Wed, 2010-06-23 at 17:06 -0400, Matthew Ku wrote: > Dear Prof

Re: [Freesurfer] DODS vs DOSS

DODS: Different offset, different slope; This models (potentially) differing slopes against the covar and allows you to check for a group- by-covar interaction DOSS: Different offset, same slope; This assumes that both groups have the exact same slope against the covar (but differing intercepts).

Re: [Freesurfer] dicom help

'dcm2nii' would be another DICOM to nifti converter to try. good luck, -MH On Thu, 2010-09-02 at 17:54 -0400, Douglas N Greve wrote: > Sorry, I don't have an easy solution. I think philips does something > that breaks our 3rd party dicom reader, so there's not an easy way for > me to fix it. T

Re: [Freesurfer] changing f.nii nframes

The 'fsledithd' utility (of FSL) can be used to edit the number of frames (as well as a host of other fields) in a Nifti file. cheers, -MH On Wed, 2010-09-22 at 09:02 -0400, Douglas Greve wrote: > Hi Tommi, that's going to be a problem because all the tools look at > the number of frames to d

Re: [Freesurfer] Surface Area and Cortical Volume

Jeff, Posting this back to the list so that others can see your reply. cheers, -MH Forwarded Message From: Jeff Sadino To: Michael Harms Subject: Re: [Freesurfer] Surface Area and Cortical Volume Date: Wed, 29 Sep 2010 17:29:45 -1000 Hi Michael, After reading your answer

Re: [Freesurfer] calculate the surface area of pial surface using mris_anatomical_stats

usage: mris_anatomical_stats [options] [] So, just end your command with the word 'pial'. cheers, -MH On Thu, 2010-09-30 at 17:09 +, Zhang, Yuning wrote: > Hi,experts, > > I am trying to get the total surface area of pial surface using the > following command,but it seems the default s

Re: [Freesurfer] calculate the surface area of pial surface using mris_anatomical_stats

2010-09-30 at 18:23 +, Zhang, Yuning wrote: > Does the surface area calculated here include the non-cortical area along the > medial wall ? > > Thank you very much. > > ________ > From: Michael Harms [mha...@conte.wustl.edu] > Sent: Th

Re: [Freesurfer] multiecho MPRAGE (MEMPR)

Hello, Deniz mentioned "T2-SPACE" rather than the multi-echo MPRAGE (memprage). Can you do something similar using the 3D T2-SPACE? cheers, -MH > Hi Deniz, > > yes, it should be in the mris_make_surfaces of that version. You need to > run it with -dura memprage_echo%d.mgz 4 > > where 4 is the

Re: [Freesurfer] Cluster Multiple Comparison Correction

Hi Jay, Permutation testing will give the most accurate results. cheers, -MH > Hi Experts, > > Which option is best to use: mc-z or perm? > I have read that perm gives more accurate results than mc-z, as it uses > the actual data rather than fake data to estimate the null distribution. > When I

Re: [Freesurfer] Cluster Multiple Comparison Correction

reesurfer Wiki is mute on the use of permutation, > unless there is some tutorial I haven't found. > How many permutations should one run? > Any other helpful hints? > > Cheers...J > > On Mon Oct 11 9:05 , "Michael Harms" sent: > > >

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