[Freesurfer] Phase-Sensitive Inversion Recovery

with PSIR sequences. Any suggestions/thoughts will be helpful. Cheers, Lena Palaniyappan This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately

Re: [Freesurfer] Phase-Sensitive Inversion Recovery

Bruce, thanks a lot. I will look forward for Jonathan's reply. On 31/10/2012 13:11, "Bruce Fischl" wrote: >Hi Lena > >sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon >Polimeni who might have some thoughts. > >cheers >Bruce

Re: [Freesurfer] hemispheric asymmetry

HI Doug Do we now have the means for computing point to point asymmetry differences between RH and LH? I remember you mentioned we may have something on this line with 5.1 Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Well

[Freesurfer] Trac-all dyld load error mac os 10.5 darwin

but the script exits when priors are being drawn. Can you help please? I downloaded the most stable version last week. (could it still be the library dependency eror?) Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Wellcome Trainin

Re: [Freesurfer] Trac-all dyld load error mac os 10.5 darwin

ion, did you by any > > chance download the snow leopard executables? > > > > a.y > > > > On Sat, 1 Oct 2011, Lena Palaniyappan wrote: > > > > > Dear Anastasia & Team > > > > > > I am running trac-all on 5.1 but my recons were

[Freesurfer] Flipped image talairach correction and missing .dcm extension

-- Hello group I am new to freesurfer. I have two problems. Please accept my apologies if these queries are bit naïve! Any help will be much appreciated. I am trying to autorecon1 a single image obtained from Philips 3T as dicom output. I use MacOS ­ X11 terminal. 1. I am not able to use mri_c

Re: [Freesurfer] Flipped image talairach correction and missing .dcm extension

o tell left from right > (it's probably why you have a flip). > > We don't have much experience with dicom. Have you tried using -it dicom in > mri_convert to be explicit about the format? > > cheers, > Bruce > > > On Thu, 30 Jul > 2009, Lena Palani

Re: [Freesurfer] combined pial and wm editing

__ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Lena Palaniyappan Clinical Lecturer &

[Freesurfer] Using segmentation for wm/pial edits

Though the pial surface and wm surface follow expected course, there are some regions that are misclassified when the colortable is overlaid. Please see the example below... Should I worry? Thanks in anticipation LKP ___ Lena Palaniyappan

[Freesurfer] Hemispheric thickness as covariate

___ Lena Palaniyappan Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could d

[Freesurfer] Pallidum too bright

? ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the

[Freesurfer] SPM-VBM and freesurfer

possible? Will I be better off doing FSL_VBM instead - if that is easy to run with freesurfer? cheers Lena Lena Palaniyappan PhD student| Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medi

[Freesurfer] MRS mask

be not projecting contrasts from a differently registered image set onto reconstructed freesurfer anatomical? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Bloc

[Freesurfer] Bbregister

I want to use contrast files that are outputs from SPM (in IMG HDR format) to overlay on inflated surfaces. But if I use bbregister and choose T1 as the image type, the regisration achieved is poor (image attached) Is this the correct way of doing this or am I missing something? Commands used:

[Freesurfer] Wmparc zero volumes

___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still co

[Freesurfer] Segmentation fault wmparc a2009s

___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the

[Freesurfer] Wmparc Destrieux atlas

\_ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software virus

[Freesurfer] Gyrification index for individual regions

I managed to obtain outputs from recon-all lGI ­ now I would like to obtain a mean gyrification index (not sure if the mean is meaningful?!) for all vertices within 3 ROIs as defined by Destrieux atlas - How should I do this? Can I treat lGI surfaces just as thockness maps ­ in which case can I us

Re: [Freesurfer] Wmparc Destrieux atlas

gz -segmentation wmparc.mgz > > which uses the default color table. > > n. > > On Tue, 2010-02-16 at 18:21 +, Lena Palaniyappan wrote: >> Dear Nick >> >> This is exactly what I have been doing for last 3 days!!! - took the last 2 >> commands and made

[Freesurfer] Local GI - euler number and compute_lgi

advance Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but t

[Freesurfer] Destrieux boundaries Insular cortex

Is there any reference available for tracking the boundaries of 5 parcellations within insula as given by Destrieux a2009s? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottin

[Freesurfer] Generating contrast images within a ROI

interested in only few of the Destrieux parcellations: is there any way I can do this? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens

[Freesurfer] Displaying parcellation labels asegstats2table

0.4520.4270.6610.6080.5311.1820.41 0.4760.4810.7770.5590.6770.5470.417 How can I get the parcellation labels displayed? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary

[Freesurfer] Buried sulci problem and freesurfer

does freesurfer handle this issue ­ I am using freesurfer to compute gyrification values: this is a major issue ­ any help will be appreciated Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( Unive

[Freesurfer] Changing roi label display color in tkmedit

I want to show a group of 5 labels ­ ach with a different color in tkmedit (Orig.mgz) display ­ can I manipulate the colors of these lables ­ I am able to do this in tksurfer: not tkmedit. Am I missing something? Cheers Lena ___ Lena

Re: [Freesurfer] Changing roi label display color in tkmedit

I don't seem to get freeview on commandline - where can I download this? Thanks LKP On 19/05/2010 17:47, "Bruce Fischl" wrote: > Hi Lena, > > I'm not sure you can do this in tkmedit. You might try freeview instead. > > cheers > Bruce > On &g

[Freesurfer] White matter volume corresponding to a surface ROI

? Cheers Lena ___ Lena Palaniyappan PhD Student & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the

[Freesurfer] Roi label mapping

values and looked at the means, I could not see the same direction of effect ­ why could this be? Is this a problem with smoothing (I used FWHM 20 for looking at whole brain comparisons) Cheers Lena ___ Lena Palaniyappan PhD student & Honorary

Re: [Freesurfer] Roi label mapping

ent slope) and DOSS (different > offset same slope) GLM analysis in qdec. Did you take this into account in > your ROI analysis? > > Cheers, > > Martin > > On Sun, May 23, 2010 at 7:09 PM, Lena Palaniyappan > wrote: >> While doing an age corrected qdec compariso

[Freesurfer] Depth of sulci from ?h.sulc

I located some discussions but could noit figure out how can I obtain numerical depth values from ?h.sulc files. I need to find the sulcal dept of certain sulci as defined in aparc.a2009 Thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still c

Re: [Freesurfer] Depth of sulci from ?h.sulc

of the movement vector > with the surface normal, although at the end the global mean is taken out > of it. Will that work for you? > > cheers > Bruce > > > On Sun, 13 Jun 2010, Lena Palaniyappan wrote: > >> I located some discussions but could noit figure out ho

Re: [Freesurfer] deepest zone in a sulcus

Hi all I am trying to determine a 'sulcal pit' - the deepest point in central sulcus. The lh.curv file gives curv values of all vertices, but how can I display the depth as a color map localised to central sulcus only? With such a display will I be able to identify the zone with maximum 'depth' a

Re: [Freesurfer] deepest zone in a sulcus

opefully lh.sulc will do the job. > > On 06/18/2010 08:49 AM, Lena Palaniyappan wrote: >> Hi all >> >> I am trying to determine a 'sulcal pit' - the deepest point in central >> sulcus. The lh.curv file gives curv values of all vertices, but how can I >>

[Freesurfer] Talairach transform failure in 7T

ena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment

Re: [Freesurfer] Talairach transform failure in 7T

not included cerebellum fully in the slices: is this a problem?) >> Thanks for your help >> >> On 08/07/2010 16:05, "Bruce Fischl" wrote: >> >>> well that certainly looks wrong. What does the original image look like? >>> On >>> Thu,

[Freesurfer] Description of frontal labels Destrieux 2009

he___defaultstructureksup/&RH=1200651 > 159612> > > Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] Replacing talairach.xfm

Hi all, How do I replace talairach.xfm by an identity matrix to prevent reorienting of images when I make-average ? Cheers Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to

[Freesurfer] Cerebellar hurdle

Is there any way I can recon-all for images that have cerebellum missing? These fail repeatedly at talairach, no-talcheck flag doesn¹t help Cheers thanks ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychi

[Freesurfer] Make_average failure

: make_average_surface +++ Any help will be much appreciated, Thanks Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottin

[Freesurfer] Coordinates for DTI tractography

should be registered to the average structural MPRAGE of the group How do I then go on to obtain the coordinates for my label on the DTI space? Many thanks Lena > > ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of

Re: [Freesurfer] Coordinates for DTI tractography

. Do you need seed coordinates in the > native DTI space of each subject or in MNI space? If MNI, which one, mni152 or > mni305? Do you need the coordinates in xyz or row,col,slice? Or do you need > your seed region to be a mask (in what space)? > > doug > > On 8/12/10 8:55 AM, L

[Freesurfer] Volume to surface dimension mismatch

I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue? Thanks Lena ___ Lena Palaniyappan Clinical

Re: [Freesurfer] Volume to surface dimension mismatch

registration > matrix, which will depend on where the volume came from. > > doug > > Lena Palaniyappan wrote: >> I have a mask file which I need to overlay on the individual images of >> a group of subjects to extract thickness values within ht mask. But >>

[Freesurfer] Mapping asymmetry on single hemisphere inflated surface

I want to compare vertexwise differences in thickness between R and L hemisphere in two groups ­ is there any workaround to create a statistical asymmetry map for this purpose? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary

[Freesurfer] Paracingulate sulcus and registration

ACC parcellated when PCS is absent, Hope someone can help Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham |

[Freesurfer] Subtracting thickness maps

words, I want to generate a single image on an average surface, that shows the regional differences between the correlated thickness maps. Is this feasible? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychi

[Freesurfer] Cortical Classifier for PALS

e.reg subjid/label/lh.PALS_Lobes.annot For this purpose. What cortical classifier file should I use to map the different PALS atlases (at least - the two of them : Brodmann and Lobes) Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Hon

Re: [Freesurfer] Cortical Classifier for PALS

Is it legit to create a .gcs file using fsaverage as the sole subject for the PALS parcellations? I intend to use this .gcs to mri_ca_label all my subjects. Please advise, Lena On 18/12/2010 13:57, "Lena Palaniyappan" wrote: I want to use the annot file for lobar areas in fsave

Re: [Freesurfer] Cortical Classifier for PALS

etter off just using mri_label2label to propagate the PALS labels to other subjects. cheers Bruce On Sat, 18 Dec 2010, Lena Palaniyappan wrote: > > Is it legit to create a .gcs file using fsaverage as the sole subject for the > PALS parcellations? > > I intend to use this .g

[Freesurfer] Getmatlab

I have MATLABR2010b, on a Mac 10.6.4, using freesurfer 5.0 I am not able to getmatlab when I invoke freesurfer Can someone help? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( Universit

[Freesurfer] LGI failure

RS at Sat Dec 25 09:23:23 GMT 2010 Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH Th

[Freesurfer] label2label error

get surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table Is there anything I can do to circumvent this? Cheers Lena ___ Lena Palaniyappan Clinical Lectu

[Freesurfer] pial surface in v5.0

f/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Darwin pmc10113.nottingham.ac.uk 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 Is there any workaround/patching? Cheers Lena ___ Lena Palaniyappa

[Freesurfer] Qdec and 3 groups GLM

es/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/label/lh.aparc.label Any help? Thanks Lena ____ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centr

Re: [Freesurfer] label2label error

On 26/12/2010 12:08, "Lena Palaniyappan" wrote: For some of my data, label2label (one of the PALS labels from fsaverage being mapped on to a subject) gives this message Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1

[Freesurfer] Bbregister for fsl tractography

Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential i

Re: [Freesurfer] effect size for cortical thickness changes

/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychia

[Freesurfer] Homologous Right Left ROIs

Hi all I have a ROI label on left hemisphere - I need to map this ROI onto right hemisphere to get a homologous region (for testing hemispheric differences). What is the best way for doing this? Cheers Lena -- Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychi

Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

t the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Lena Palaniyappan

Re: [Freesurfer] LGI error in make_outer_surface at 31

Hi Lisa Are you able to see the paths traced from the 'intermediate' files - you can find them in a tmp folder within the subject's surf directory Lena On 04/04/2011 16:24, "Lisa Ronan" wrote: Dear List I have recently come up agains the same problem as described below, namely the error w

[Freesurfer] parcellating pial surface for surface areas

Hi all is it possible to obtain the surface area computations for each of the parcellations in Destrieux annot from pial instead of white surfaces? As the vertex addresses are likely to be different between white and pial surfaces, I suppose the following command is not appropriate - any ideas